The Christian thing didn't technically make sense...
*spoilers*
Yes, yes- it's in folklore. So are trolls who wear clothes and communicate with people- but the film specifically says to dismiss fairy tales.
Now, things like why they turn to stone, how the co-exist, how they blend in to their environment are all pretty well explained and kept as scientific as possible- which might be why it's so nagging. They make such a point in some scenes to show how their existence can make sense that this one thing singles out as making the least sense.
Faith doesn't change blood chemistry. There's no reason for a troll to tell the difference between Christian music and non. It just seems weird to suck all the mysticism out of trolls and leave that in there.
Don't get me wrong- this movie was awesome, and I definitely laughed at a few of those scenes (like when he blasts the Christian music to distract it), just saying that stood out a bit.