A couple of years ago I looked over the alignment software used in a bunch of genetics studies and spotted a pretty trivial mistake that caused mis-alignment of the strings. This in turn led to wrong conclusions about the order in which mutations took place. This sort of thing is probably quite common: biologists are not computer programmers (though the combination is for sure occurring), they tend to treat the computer programs in roughly the same way as they would treat lab equipment, stuff goes in, other stuff come out. If it looks good and seems to work then it probably is good.

But the complexity of the software is such that you need to check very carefully whether or not the software operates in the way you expect it to.