Just as in real life there are several things possibly happening when your coach calls a timeout. It could be called so your top players can rest for a bit and play better afterwards. It could also be that your coach is trying to make adjustments to your offense/defense in general, something along the lines of putting a double-team on a guard who is torching you. Towards the end of games you'll get the typical clock stoppage timeouts where the coach will try to design a set play to give you a quick - hopefully high percentage - shot. Substitutions as well are yet another reason.
The match engine isn't perfect, but overall it does a very good job of simulating real situations. If something happens in a game on BB, look for why it may have happened in a real game and more times than not you'll be pretty close to your answer.