Did St. Augustine warn us about interpreting the Bible in a way which harms science?

A simple web search shows the quote is accurate, as it is shown in Catholic sites:

But the hermeneutics of Augustine merit great praise, especially for their insistence upon the stern law of extreme prudence in determining the meaning of Scripture: We must be on our guard against giving interpretations which are hazardous or opposed to science, and so exposing the word of God to the ridicule of unbelievers (De Genesi ad litteram, I, 19, 21, especially n. 39). An admirable application of this well-ordered liberty appears in his thesis on the simultaneous creation of the universe, and the gradual development of the world under the action of the natural forces which were placed in it. Certainly the instantaneous act of the Creator did not produce an organized universe as we see it now. But, in the beginning, God created all the elements of the world in a confused and nebulous mass (the word is Augustine's Nebulosa species apparet; "De Genesi ad litt., " I, n. 27), and in this mass were the mysterious germs (rationes seminales) of the future beings which were to develop themselves, when favourable circumstances should permit. Is Augustine, therefore, an Evolutionist?

You should find the quote in that book. There are other similar translations of perhaps his selected commentary on Genesis, which does not have that quote, but show relevant insight about his views on Genesis. It is fascinating to see that Augustine, living in the age of Science, interpreted Genesis as a mystical scientific book, and failed to see so clear symbolism, and seemed to have no understanding of the Jewish literature. He also failed to see that the scripture are written by men. He held the exact same view of inspiration as modern men hold today, that God directly inspired them as oracles and dreams, depicting exact literal descriptions of events. This is the only reason behind his inability to ever come to a definite conclusion on the meaning of days in the creation account.

Reading about his commentary of Genesis and conversion, it seems we are reading about a conversion of a modern Atheist turned apologist in the western world. He was more of a philosopher than a theologian, who seemed to have converted to Christianity which was convenient to his physical scientific world-view. I agree with his views that denying science and supporting any ludicrous beliefs such as denying evolution, leads people away from God, and those who work against common sense are actually harming the evangelical mission. I have read similar things from Dr Craig from reasonablefaith.

Did St. Augustine warn us about interpreting the bible in a way which harms science?

It is not so much that St. Augustine is warning us against interpreting Scriptures in a way that harms science, but rather he is admonishing us to be careful not to interpret Sacred Scriptures in a way that goes against science and thus the learned men of proven scientific research would make sport of such nonsense and by consequence the Scriptures (Bible) and the Christian religion in general.

St. Augustine’s De Genesi ad Litteram—Libri Duodecim (The Literal meaning of Genesis—A Commentary in Twelve Books) was borne out of a desire to present a more literal understanding of Genesis, setting it in its proper historical sense. The literal interpretation however for St. Augustine had limit the should be respected!

It could be said that St. Augustine’s thinking could be compared to Galileo Galilei‘s now famous phrase: The Bible shows the way to go to heaven, not the way the heavens go.

Here are a few phrase of St. Augustine that would put his ideas into proper perspective:

We must be on our guard against giving interpretations that are hazardous or opposed to science, and so exposing the Word of God to the ridicule of unbelievers. — Saint Aurelius Augustinus Augustine (Genesis in the Literal Sense)

...it is not to be taken in the sense of our day, which we reckon by the course of the sun; but it must have another meaning, applicable to the three days mentioned before the creation of the heavenly bodies. — Saint Aurelius Augustinus Augustine (iv.26)

That day in the account of creation, or those days that are numbers according to its recurrence, are beyond the experience and knowledge of us mortal earthbound men. And if we are able to make any effort towards an understanding of those days, we ought not to rush forward with an ill considered opinion, as if no other reasonable and plausible interpretation could be offered. — Saint Aurelius Augustinus Augustine (iv.44)

Science Quotes by Saint Aurelius Augustinus Augustine

That's not exactly what St. Augustine said.

De Genesi ad Litteram pp. 186-7 (lib. 1 cap. 19 n. 39):

…it frequently happens that even non-Christians will have knowledge of this sort in a way that they can substantiate with scientific arguments or experiments. Now it is quite disgraceful and disastrous, something to be on one's guard against at all costs, that they should ever hear Christians spouting what they claim our Christian literature has to say on these topics, and talking such nonsense that they can scarcely contain their laughter when they see them to be toto cœlo ["all heavens"], as the saying goes, wide of the mark. And what is so vexing is not that misguided people should be laughed at, as that our authors should be assumed by outsiders to have held such views and, to the great detriment of those about whose salvation we are so concerned, should be written off and consigned to the waste paper basket as so many ignoramuses.

Whenever, you see, they catch out some members of the Christian community making mistakes on a subject which they know inside out, and defending their hollow opinions on the authority of our books, on what grounds are they going to trust those books on the resurrection of the dead and the hope of eternal life and the kingdom of heaven, when they suppose they include any number of mistakes and fallacies on matters which they themselves have been able to master either by experiment or by the surest of calculations? It is impossible to say what trouble and grief such rash, self-assured know-alls cause the more cautious and experienced brothers and sisters. Whenever they find themselves challenged and taken to task for some shaky and false theory of theirs by people who do not recognize the authority of our books, they try to defend what they have aired with the most frivolous temerity and patent falsehood by bringing forward these same sacred books to justify it. Or they even quote from memory many things said in them which they imagine will provide them with valid evidence, not understanding either what they are saying, or the matters on which they are asserting themselves (1 Tm 1:7).

Augustine of Hippo (354-430) did not live in the Age of Science, as we do today. Nor was the word 'science' yet coined in any language, so any translation of his words which pops in 'science' is not using a word he would have used. Translators are sometimes at risk of assuming that a word we use today is equivalent to an ancient one, as in Latin or koine Greek or biblical Hebrew. That has happened with our comparatively modern word 'science', which we now take to mean a disciplined methodology to discover how things in the natural world 'work', proven by repeatable experiments. (I know that's not a dictionary definition, but I wish to make a point.)

So, what did Augustine refer to, in that quote? Here is another one from the same book. From this, we can grasp what he had in mind when modern people have in mind scientific, verifiable experimentation:

"Usually, even a non-Christian knows something about the Earth, the heavens and the other elements of this world... Now, it is disgraceful and dangerous thing for an infidel to hear a Christian, presumably giving the meaning of Holy Scripture, talking nonsense on these topics... People outside of the household of the faith think our sacred writers held such opinions, and... if they find a Christian mistaken in a field which they themselves know well and hear him maintaining his foolish opinions about our books, how are they going to believe those books in matters concerning the resurrection of the dead, the hope of eternal life, and the Kingdom of Heaven?" The Literal Meaning of Genesis, Vol. 1, translated by J.H. Taylor (New York: Paulist Press, 1982)

There he has in mind knowledge of the Earth, the heavens, and elements of this world. This quote agrees with the one given in the question. In his day, and up until the coining of the word 'science', the phrase 'natural philosophy' would have been used. In this related quote, Augustine has in mind the way in which the natural world functions as a system of signs. We would call that 'semiotics' today, but that modern word will no more be found in Augustine's writings than the word 'science'.

"Some people read a book in order to discover God. But there is a greater book - the actual appearance of created things. Look above and below you, and note and read. The God that you want to discover did not write in letters of ink, but put in front of your eyes the very things that he made. Can you ask for a louder voice than that?" Sermons 68, 6, Augustine of Hippo

Those two quotes show how - in what sense - Augustine warned about interpreting any books about natural philosophy in a way that shows up Christian ignorance on the topic. He advocates looking at the "book" of God's creation which is visibly all around us, to "find" (by observation) what can be known of God there. He even gives the impression of considering the natural world to be more powerful a witness to God than the written Holy Scriptures!

The answer is the other way around to how it's posed in the question. Augustine was concerned that Christians uttering nonsense about the known natural philosophy of his day would prevent non-Christians from then listening to them about biblical doctrines such as "the resurrection of the dead, the hope of eternal life, and the Kingdom of Heaven"