Oh yes, there are tons of plotholes in MLPIT. Not to mention some contradictions/inconsistencies with other games (i.e. E. Gadd's back-story).
Anyway, I gots some more stuffs added:
MLPIT (Past) alludes to LM:
~After Young Gadd's lab on Thwomp Volcano is destroyed, he says, "I hear there's an affordable lab at the edge of the Boo Woods. I think I'll relocate there for a time. I have a hankering to do some paranormal research."
SM64DS foreshadows LM?:
~If Luigi defeats him, King Boo says, "I just love the look of terror on your face! In fact, I live for it! Eee hee hee! See you soon!"
PM references SMB:
~Goombario's Tattle of Goombas: "These guys are old school. They've been around since you were in Super Mario Bros.!"
Other information [Paper Mario]:
~Goombario's Tattle of Koopa Troopas: "Is it only my imagination or did Koopa Troopas used to walk around on four legs? I guess that was a really long time ago, huh?"
Koopa Troopas walked on all fours in SMB, SMB2J/LL, SMB3, SML2, and Mario Clash. They began walking upright in SMW, and have, for the most part, been that way ever since. SMG is an interesting exception, and so far is the only game released after PM to have quadruped Koopa Troopas. Troopeas in MLSS and Electro-Koopas from SMS walk on all fours, but they seem to be either different or sub-species. Interestingly, Koopas walk upright in prequel games like YI and MLPIT (Past).
~Goombario's Tattle of Lakitus: "It seems like these Lakitus have been hassling you for your entire career, Mario." By release date, Lakitus first appeared in SMB.
~In one of the rooms in Dry Dry Ruins, Goombario says, "Now that I've helped you find Dry Dry Ruins, will I become famous, too? You don't care. You're already a household name." Mario is apparently already famous. Although this may or may not be breaking/leaning on the fourth wall.