I'm having the same problem with a different Chinpokomon. I didn't get either of the ones from the school. I was able to get one of them, but the other one is on the second story and the doors just lock up...it doesn't make sense. You even had to blow open the door for Tweek and Token to get in...but the doors are all locked after the mission in the school is complete.
I'm definitely not reloading a save point that takes off 7 hours because of one Chinpokomon.