There are a few reasons your cream puffs might collapse or not puff up properly in the oven. The first is that you may not have cooked out the moisture enough. Make sure you give it a full 2 minutes on the stove. The second is that there is no way for the steam to escape when the puffs are baked. To avoid this I poke a hole in the side of each puff with a knife as soon as they come out to let the steam out.