Hello, Gafflosion!
Thank you for contacting Pixelmon Bug Tracker Service.
From Pixelmon 8.2.0, we added the TMs by each generation. Therefore, if you use the old generation TM to the new generation pokemon, the TM will be breaking down without teaching the move.
For example: I have bidoof and I want this bidoof to learn Substitute, so I use TM_Kanto_Substitute to this bidoof. If you do this, it will not teach the move and the TM will be breaking down. If you want to teach the Subsitute to Bidoof you must use the TM from 4th generation-7th generation. You can check the infromation by checking the list of TM from the Pokemon's move stats.
Bidoof move list GUI:
https://imgur.com/a/GZip4z2If the problem is not related to this, please provide more information about the issue.
Have a wonderful day :)