it kind of bothered my that mickey didnt put two and two together when he met apprentice xehanort. the name and silver hair should have been a big clue. xehanort isnt a common name and im sure yen sid told mickey at some point what he looked like
While it isn't common, it's also not said to be unique, and Mickey did see Master Xehanort in person when he went to the final battle in BBS, so he knows that he's an old geezer who is
bald and has golden eyes. Apprentice Xehanort though is much younger, has silver hair and
brown eyes, so while Mickey might have had some suspicions (as the journal in KH 2
does state meeting the apprentice somewhat disturbed the King) he didn't automatically assume the worst. He didn't even assume the worst with Ansem SoD, who blatantly wears MX's attire and clearly scolds himself in DDD for being "so blind" to not see the issues at hand.
Mickey did (and wanted to) believe that the sacrifices made by Terra, Aqua and Ventus put an end to the threat of Master Xehanort, so he might in part not even
wanted to believe that this could be the same Xehanort, because it would also mean that all the suffering and sacrifice made by TAV would have been in vain.
It ultimatively was exactly like this, but like Ansem the Wise blinded by his thirst for vengeance refused to acknowledge that Nobodies could indeed grow hearts and that Roxas and Naminé had real feelings, Mickey in his grief about not being able to save TAV refused to acknowledge that Master Xehanort could be again behind everything.
This is also strengthened more by his reaction in the secret ending of Re: Coded when Yen Sid speaks about what Xehanort might plan next.
Mickey interjects that Xehanort should be gone since Riku and Sora defeated both Ansem and Xemnas in KH 1 and 2, indicating that despite being a Keyblade Master Mickey does not know that the destruction of a Heartless and corresponding Nobody results in the rebirth of the original persona until Yen Sid explains it in that very cutscene.
Maybe Mickey didn't want to think the worst. AtW is a good friend of his, and might be insulted if he thought bad of his apprentice.
That may be actually a factor too, Mickey isn't the type to be immediately suspicious of everything.