Doubts and Meditation

This is called state of confusion( शंका or संदेह in hindi).

It usually arises due to lack of oxygen in brain. You need physical exercise like jogging or yoga in Open(not in Gym) area.

When Meditator put focus on breathing, s/he might put too much pressure without awareness of such. This pressure can be felt inside wind-pipe ,nearby Adams apple. Pressurized sticking of tongue with muscles behind upper jaws can also be observed. Brain might feel like heavy.

Good blood circulation, 1st exercise in fresh air then do meditation will help. Otherwise, good to do some free service involving hard physical work in shifts with meditation work.

There is a wonderful sutta, SN24.4, which discusses stream-entry and beyond:

sn24.4: ‘It might not be, and it might not be mine. It will not be, and it will not be mine.’

sn24.4: What do you think, mendicants?

sn24.4: Is form permanent or impermanent?”

sn24.4: “Impermanent, sir.” …

And one of the interesting things about meditation is that one notices that very impermanence. Yes, doubts will arise. And just as surely they will fade away and disappear all on their own.

Unless you follow them.

But if you just watch them, minding your breath, you may notice that the breath keeps going while the doubts come and go. With constant awareness of breathing, we become more satisfied and settled in the impermanence of doubt. We become less prone to pursuing doubts. We simply just breathe and meditate.

What is to remedy as long as you don't cling to the doubt? If you practice with momentary concentration then you see the doubt come and go. You won't see the doubt if you are too concentrated. If your attitude is, "Well, there it is, that's what is there" then there is no attitude of clinging. There is nothing to do. There is no distraction because the distraction is what is.

A doubt is no different than a pain in your knee, a loud noise, or a cold room. Simply turn your attention back to your object of meditation and any doubt will disappear on it’s own. The only things that take us out of concentration are the things we give attention to. Pay them no mind.

Meditation teaches the mind to avoid obstacles. Over time, these things will lessen or cease to arise entirely.

Anapanasati will distance you from those thoughts due to exertion of effort to create a wholesome state by stilling the unwholesome formations. When you attain the first jhana thinking about doubt will be stilled on account of the power of wisdom, power of exertion and power of composure.

The distance is a thing and a wholesome is close to the wholesome and it is far from the unwholesome. Details on this are in the Abhidhamma.

The stilling of doubt can be tricky but the memorizing of expression so that one can penetrate the meaning is to an extent a must do.

Here on doubt from Sutta and the Vsm;

Doubt

A. Nourishment of Doubt

There are things causing doubt; frequently giving unwise attention to them — that is the nourishment for the arising of doubt that has not yet arisen, and for the increase and strengthening of doubt that has already arisen.— SN 46:51

B. Denourishing of Doubt

There are things which are wholesome or unwholesome, blameless or blameworthy, noble or low, and (other) contrasts of dark and bright; frequently giving wise attention to them — that is the denourishing of the arising of doubt that has not yet arisen, and of the increase and strengthening of doubt that has already arisen.

Six things conducive to the abandonment of doubt are as follows:

1. Knowledge and pondering of the Dhamma
2. Asking questions about the Dhamma
3. Familiarity with the Vinaya (the Code of Monastic Discipline, and for lay followers, with the principles of moral conduct)
4. Firm conviction concerning the Buddha, Dhamma and Sangha.
5. Noble friendship
6. Suitable conversation

In addition, the following are helpful in conquering Doubt: Reflection, of the factors of absorption (jhananga); Wisdom, of the spiritual faculties (indriya); Investigation of reality, of the factors of enlightenment (bojjhanga).

C. Simile If there is a pot of water which is turbid, stirred up and muddy, and this pot is put into a dark place, then a man with a normal faculty of sight could not properly recognize and see the image of his own face. In the same way, when one's mind is possessed by doubt, overpowered by doubt, then one cannot properly see the escape from doubt which has arisen; then one does not properly understand one's own welfare, nor that of another, nor that of both; and also texts memorized a long time ago do not come into one's mind, not to speak of those not memorized — SN 46:55

You can practice the 4 Foundations of Mindfulness:

These, bhikshus, are the four focusses of mindfulness that are to be cultivated for the abandoning of these five mental hindrances.

(Satipaṭṭhāna) Nīvaraṇa Sutta

Also,

one understands and sees, as it really is, one’s own benefit,

one understands and sees, as it really is, others’ benefit,

one understands and sees, as it really is, the benefit of both

(Nīvaraṇa) Saṅgārava Sutta

One also can try developing the 7 Enlightenment Factors to overcome it. See: Āvaraṇa Nīvaraṇa Sutta

Wise attention can be used to overcome dought:

Bhikshus, no other single thing do I see, on account of which unarisen doubt does not arise, and arisen doubt is abandoned, as on account of this, bhikshus, namely, wise attention.

Bhikshus, through wise attention, unarisen doubt does not arise, and arisen doubt is abandoned.

Nīvarana,pahana Vagga

Also, do not feed dought. See: (Nīvaraṇa Bojjhaṅga) Ahara Sutta

Also see: Nivarana and Vicikiccha by Piya Tan