Fixed in latest commit, thanks for reporting
https://github.com/kwsch/PKHeX/commit/d8f064409f9ce2aadcc214cb4884795ded7bccee
For your illegal moves, it's behaving correctly. I assume it still has Crystal met data, which would have been wiped on transfer 2->1. Having Crystal met data implies it's never visited RBY, thus can't learn those moves.