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.
I'm currently at 29/30 chinpokomon and the last one that I need is Pterdaken...but the problem is that he's on the second floor of the school that's unreachable after the missions at the school have been completed. Not a big deal...but the doors to the school are locked after you've completed all the missions inside of them. It would make sense for things like the UFO to be unreachable after the missions are done (since it blew up)...but the school is still accessible. Those doors weren't even locked when you first saw them and you even blew the front door open so that Token and Tweek could get in, but they lock after you beat the game? That doesn't make sense. Please either open those doors or allow another way to get that Chinpokomon...it doesn't make any sense that they should be locked after the story has been complete.