Now as I said, I never caught Missingno. But I did use the Duplicate Item trick several times. Is there a way to fix this? I think there is something else glitchy with the game, but I haven't played it in so long, that I don't
This is because the transform attack uses the same hex data as a recoded attack used by a removed Kangaskhans ghost sprite. During the localization of Red/Blue, there were patches made to fix a few oversights, but either as a result or because it wasn't noticed, one of the flags would corrupt Dittos transform attack if certain criteria were met (such as getting MissingNo. through the old man glitch.)
What you essentially did by accident (presumably) was trigger a defunct battle flag much like using missingno. that causes the game to glitch out. Since the command string effects attacks, there are going to be issues with battling on that save file. The best thing you can do is start a new save since there's no way to fix it outside of reverse engineering your game data and going through individual strings.