There are some points where science is in conflict with the Abrahamic religions as traditionally understood. These points have been exhaustively discussed elsewhere by other people. There are also some points where science is in conflict with the conventional ideas of 'secular humanism'. These do not usually seem to have been discussed from a scientific perspective.
The first is that science is absolutely unambiguous about 'when life begins'. An individual, genetically distinct, human being as defined by science comes into being over a brief period of time in which a series of chemical events called 'conception' occur. From this point forward it has a very good chance (at least 10%, possibly greater) of experiencing the sense impressions of the universe that we associate with living a human life - if it is left alone. The suggestion that it is 'part of the mother's body' at any stage of its existence is a relic of pre-Renaissance science.
We can ask ourselves 'which human beings should we treat decently?' and it might be possible to reach different answers to that question. But scientifically, individuated human beings exist from conception. It is not a question above anybody's pay grade.
The second is that the universe has to be part of something bigger - which we can call 'The Universe'. Something has to be self-existent: that is, to just be. But our universe cannot be that thing - the Second Law of Thermodynamics tells us that it is clearly 'running down', and there is a wealth of circumstantial evidence is that it had a beginning at some particular point in time. We don't know anything about what The Universe is like. Anything.
Saying that the universe leapt into existence out of nothing in a quantum fluctuation is doing violence to the concept of nothing- assuming the existence of a Universe where the laws of quantum physics hold.