A seeming contradicion in meditation

It appears you got some misinformation. Buddha taught that there are wholesome and unwholesome pursuits performed by body, speech, and mind.

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Then King Yama says, 'My good man, through heedlessness you did not do what is good with body, speech, & mind. And of course, my good man, they will deal with you in accordance with your heedlessness. For that evil kamma [2] of yours was neither done by your mother, nor done by your father, nor done by your brother, nor done by your sister, nor done by your friends & companions, nor done by your kinsmen & relatives, nor done by the devas. That evil kamma was done by you yourself, and you yourself will experience its result.'

https://accesstoinsight.org/tipitaka/mn/mn.130.than.html

Imagine that you have received ownership of a garden, and you have came to see it.

It looks horrible in all possible ways. Disarray and garbage everywhere. It couldn't serve its purpose well in its present state.

Now, is there something wrong with the garden?

Not at all; there are no ghosts, aliens or supernatural forces; the garden have came to that state according to its causes and conditions.

But it might need some work if it should feed people.

When we mature in Dharma practice, we stop worriying about things being wrong, because we see that they happen in accordance with causes and conditions.

We just work with those causes and conditions, arranging them in more efficient manner.

PS (Edit 28.10.2020:)

In other words, Dharma is not for making us into something else.

Practice is not for doing anything with ourselves.

Doing something with ourselves is the position of manipulations based on the image of self. As long as we keep it, there is no actual wholeness or freedom.

Case 19 of the Mumonkan
Nansen's "Ordinary Mind Is the Way"

Jõshû asked Nansen, "What is the Way?" "Ordinary mind is the Way," Nansen replied. "Shall I try to seek after it?" Jõshû asked. "If you try for it, you will become separated from it," responded Nansen. "How can I know the Way unless I try for it?" persisted Jõshû. Nansen said, "The Way is not a matter of knowing or not knowing.

Knowing is delusion; not knowing is confusion. When you have really reached the true Way beyond doubt, you will find it as vast and boundless as outer space. How can it be talked about on the level of right and wrong?"

With these words, Jõshû came to a sudden realization.

Mumon's Comment

Nansen dissolved and melted away before Jõshû's question, and could not offer a plausible explanation. Even though Jõshû comes to a realization, he must delve into it for another thirty years before he can fully understand it.

Mumon's Verse
The spring flowers, the autumn moon;
Summer breezes, winter snow.
If useless things do not clutter your mind,
You have the best days of your life.

One thing I really enjoy doing is sitting in the woods. I'll hike out to some spot, doesn't really matter where, throw down a poncho or, if it's dry, just plop my butt right down on the duff. I'll usually sit there for the better part of an hour, sometimes longer. It really depends on the day. It's really interesting to see what happens as you sit there for an extended period of time. At first, the woods are completely silent. No bird flits or animal stirs. I mean, let's be honest, you scared the bejesus out of them as you came barreling into their home with your heavy hiking boots. After about fifteen minutes, though, you'll start to hear a few chipmunks chirp and robins chatter. After twenty five minutes, the chickadees move back in. Soon after the squirrels and the nuthatches return. Sit there long enough, completely still, and after forty five minutes, it's not that uncommon to have birds start landing on you or to have a squirrel scurry over your foot. Sit there for an hour or longer and maybe you even see a bear or a fisher.

Your mind is a lot like the woods. Meditation is a lot like sitting in the forest. At first, there's just too much that's been churned up. All of that detritus clouds our senses. Just like the woods we see at first isn't the woods in its baseline state, so to is our day to day mind a completely divorced from our true, ordinary mind. Sit long enough, and all of that nonsense begins to fall away. (Oddly, it follows about the same schedule!) Sit long enough and there's no telling what you'll wind up seeing. That's half the fun. We don't know what will appear - in the woods or in our meditation.

What effort was there in my sitting in the woods? Did I lure the birds back in? Did I hunt them down and drag them into that glade with me? Was I doing some magical ritual that resulted in that junco landing on my boot? Of course not. If I did any of those things, those creatures would just run farther away. They were drawn in by my non-effort. They were attracted to my ordinary mind, plain and undisturbed. When we sit in meditation, we just sit. Our mind falls onto one spot like a leaf falls onto water. We do not press it there. It's held aloft by the calmness of the waters below. Any coming or going, goal, or destination will sink us.

Where is there any effort?

The answer to your question is that it is not what thoughts you think, but how you think them. The thoughts that arise come from your mental basis. From it you think a certain way. Your basis determines if you like or dislike the thoughts which arise. Practicing Sila and Metta will change, transform, your basis and better thoughts will then arise. If hatred or ill will are present in your feeling, then Metta practice will change your basis and these feelings dissolve and simply won’t rise again, as long as you keep up the practice.

Buddhism teaches there is wrong thought, as follows:

And what is wrong resolve? Being resolved on sensuality, on ill will, on harmfulness. This is wrong resolve....One makes an effort for the abandoning of wrong resolve & for entering right resolve: This is one's right effort. One is mindful to abandon wrong resolve & to enter & remain in right resolve: This is one's right mindfulness. Thus these three qualities — right view, right effort, & right mindfulness — run & circle around right resolve.

MN 117

The path of Buddhism is about making an effort to change wrong thought into right thought, as follows:

And what, bhikkhus, is right effort? Here, bhikkhus, a bhikkhu generates desire for the nonarising of unarisen evil unwholesome states; he makes an effort, arouses energy, applies his mind, and strives. He generates desire for the abandoning of arisen evil unwholesome states…. He generates desire for the arising of unarisen wholesome states…. He generates desire for the maintenance of arisen wholesome states, for their nondecay, increase, expansion, and fulfilment by development; he makes an effort, arouses energy, applies his mind, and strives. This is called right effort.

SN 45.8

Bhikkhus, before my enlightenment, while I was still only an unenlightened Bodhisatta, it occurred to me: ‘Suppose that I divide my thoughts into two classes. Then I set on one side thoughts of sensual desire, thoughts of ill will and thoughts of cruelty, and I set on the other side thoughts of renunciation, thoughts of non-ill will and thoughts of non-cruelty.

As I abided thus, diligent, ardent, and resolute, a thought of sensual desire arose in me. I understood thus: ‘This thought of sensual desire has arisen in me. This leads to my own affliction, to others’ affliction, and to the affliction of both; it obstructs wisdom, causes difficulties, and leads away from Nibbāna.’ When I considered: ‘This leads to my own affliction,’ it subsided in me; when I considered: ‘This leads to others’ affliction,’ it subsided in me; when I considered: ‘This leads to the affliction of both,’ it subsided in me; when I considered: ‘This obstructs wisdom, causes difficulties, and leads away from Nibbāna,’ it subsided in me. Whenever a thought of sensual desire arose in me, I abandoned it, removed it, did away with it.

As I abided thus, diligent, ardent, and resolute, a thought of ill will arose in me…a thought of cruelty arose in me. I understood thus: ‘This thought of cruelty has arisen in me. This leads to my own affliction, to others’ affliction, and to the affliction of both; it obstructs wisdom, causes difficulties, and leads away from Nibbāna.‘ When I considered thus…it subsided in me. Whenever a thought of cruelty arose in me, I abandoned it, removed it, did away with it.

MN 19

There's no contradiction. Questions such as this one arises when trying to understand Buddhism and meditation from an intellectual point of view, which is not really possible due to the depth and profundity of the Dhamma.

Go practice meditation and questions such as these naturally get answered and settled.

This question belongs to the 5th mental Hindrance about Doubt (vicikiccha)

I can't seem to reconsile these two thoughts.

Expressing thoughts as "your thoughts" may be a source of vexation. There is a possessiveness here that can be relinquished--they're just thoughts. Relinquishing the possessiveness here, meditation becomes tranquil:

SN35.246:4.25: As they search in this way, their thoughts of ‘I’ or ‘mine’ or ‘I am’ are no more.”

The work of meditation is to ease the clutching grasp of "I and mine." That clutching grasp, that grasping is dangerously vexing.

SN35.246:1.6: Any monk or nun who has desire or greed or hate or delusion or repulsion come up for sounds … smells … tastes … touches … thoughts known by the mind should shield their mind against them: ‘This path is dangerous and perilous, thorny and tangled; it’s a wrong turn, a bad path, a harmful way. This path is frequented by bad people, not by good people. It’s not worthy of you.’ The mind should be shielded from this when it comes to thoughts known by the mind.

Reconciling thoughts is basically just assessing them: "do I want this thought or not?" This assessing is actually suffering. This assessing is a possessiveness towards thoughts. There is a craving for "good thoughts to be possessed" and "bad thoughts to be avoided". Give up the possession and simply notice that thoughts disappear on their own and bubble up on their own. There is no need to possess them.

DN15:9.1: So it is, Ānanda, that feeling is a cause of craving. Craving is a cause of seeking. Seeking is a cause of gaining material possessions. Gaining material possessions is a cause of assessing. Assessing is a cause of desire and lust. Desire and lust is a cause of attachment. Attachment is a cause of possessiveness. Possessiveness is a cause of stinginess. Stinginess is a cause of safeguarding.

Thoughts are impermanent and unsatisfactory.