In most cases, the conflicts that arise from the daily encounters people have between Torah and science are based on misunderstandings.
Often it is a mistake about Torah–and people end up trying to defend the sheer nonsense that they, for some strange reason, believe is Yiddishkeit.
These people find they cannot continue with their religion because they think it is ridiculous.
In fact, their "religion" is indeed ridiculous.
When I was a young man, I met someone in Israel who was then a very important political personality (interestingly, he was son of a famous rabbi, a member of the Mo'etzel Gedolei HaTorah in Poland).
We were talking, and he asked me, "Where does God put his legs?"
For a moment I thought he was joking, but he wasn't.
When I tried to tell him that, as far as I knew, God has no legs, he told me I did not know what I was talking about, because his father truly believed that God has legs!
I tried to remonstrate.
I opened the Siddur and showed him that not only do we not believe that, but we should not: it is forbidden.
He ended the conversation by telling me that he was very friendly with the rosh yeshivah of Mir, and that he would warn him that there was a person in Jerusalem who should be destroyed.
In a certain way, this conversation is typical of the "Torah u-madda" (Torah and science, secular knowledge, philosophy) clashes that many people experience.
Often they have an encounter, not only of bad science with Torah, but of bad science with bad Torah.
That becomes a much more dangerous encounter, because a person may try to defend something that is entirely untrue.
With regard to Torah concepts, many people have never progressed beyond kindergarten, and their theological concepts remain on this elementary, even infantile level.
It is therefore no wonder that some people spend years creating and defending imaginary points of belief against imaginary attacks by science.
In many cases, a whole generation is still defending positions that were espoused by apologetic writers a century ago.
Many words and concepts that have become taboo in religious society have nothing wrong with them except for the fact that 50 or 100 years ago, people for some reason thought them to be problematic.
People see problems because they are defending all kinds of old incorrect positions.
–Rabbi Adin Steinsaltz
From the essay, "Where do Torah and Science Clash?" in A Dear Son to Me by Rabbi Adin Steinsaltz