I'm going to just get out from hiding again...
Did you use one of the ??? spaces between Celebi and Treeko for Swampert X? If you did, and if I remember correctly because I worked with (well not really working, but I did give a lot of support and advice) Pokemon Advance Adventures (proof of me supporting and giving ideas is on the credits section, but you probably don't care anyway) and the tyrant pokemon were replaced with said ??? spaces, you couldn't add pokedex entries to those spaces I believe so they just became registered as Rattata. You really can't fix the bug/oddity, unless you replaced another pokemon for Swampert X, but like you said, it does not affect anything.
Anyway just thought I'd let you know what the problem was, just to give you a tiny bit more knowledge on rom-hacking (even though you are so much better then me xD). Good luck on your hacking projects and I promise I will play them, I always played Adventure Red's betas anyway.