The beast cells were much more secure than the one Villin and Elinoire were in. The one they were in was intended for those that aren't quite a proper magus yet, even though it was easily capable of keeping a group of people like that, magical beasts were different.
The magical beasts captured here are those that either have unknown bloodlines or rare and powerful ones. Either way, they were hard to contain.
Each beast had three layers of security at the least, so that if the guards that went to grab them got knocked out, there were still multiple doors between them and the rest of the facility. Some of these fought every time they went to get them for experiments, making them very hard to control.
It would take time to break into one of the cells. Even with transfiguration, it would take Villin about ten minutes to enter one of the cells, this was partially due to his weak foundation in the art.