I imagine that keeping great number of ghost stunned must be huge pain.
The main thing is, you'll need to keep track of all the bug-eyes and don't leave sleeping ghosts around, because they start wandering about. I usually pick them up and at least put those outside or on the ground floor in a couple of piles and have agents guard the pile.
Here's a few tips about the training opportunities in the mission:
- melee weapons (especially electric club); for maximal training, it's actually a good thing that the ghosts wake up, so you can stun them again!
- collecting a few ghosts in a pile and pepper spraying (increases bravery) or boom boxing (increases reactions and throwing) them; at this point of the game it's up to RNG whether you have obtained them. (The more enemies you have within the range of an area effect, the more experience you get.)
- even throwing grenades especially at the beginning of mission can be useful; I always go to the mission with two preprimed grenades per agent and throw them at the big 2x2 ghosts; you can also drop grenades on bug-eyes you've stunned if you don't want to deal with them again (takes 2-3 grenades)
- while shooting is rather ineffective with kinetic guns, it is still good for training (because you can shoot the maximum times without killing the opponents). You can also shoot the stunned bug-eyes and perhaps even kill them by standing on top of the square and shooting at the same square (= shoot downwards).