So in other words, the lab abducted Pokemon so that abducted people can abduct them... and possibly help out in a possible break out?
When you put it like that.. It does sound kind of dumb. Okay, new idea. Maybe instead, we could have some wild Pokemon loose in the lab blimp that these crazy science people had no idea about. Like, some of the rooms have to be camera-less, right? Of course, a wild Pokemon has to eat and all, so maybe they've been stealing from a food storage room in the blimp or whatever. A trainer would eventually find them, and I don't really know about the whole Pokeball part, but the wild Pokemon could be friendly enough to help the trainer out for a while. Later on, maybe that trainer will find a Pokeball if they break into some room. (Kind of like Team Rocket Hideout. You explore more than you have to, so you get items that were sitting around.) Of course, then the trainer may catch the Pokemon or just keep it for later or whatever.
At least, that's the best thing I can come up with that would enable people to get more Pokemon. Maybe it's too far-fetched, though?