Didn't the Lugia arc reference the events of the second movie? I mean, Ash and James mentioned their seeing a Lugia in the Orange Islands when they first saw Silver.
Also, I think I recall someone saying on a debate thread similar to this on Serebiiforums that Ash and Brock recognized Celebi, and May and Max didn't in the Green Guardian, plus they had Ash say that he "Met" suicune (yes he did see it in "Don't Touch that Dile", but he said that he met it, which implied that he got to know it, and the only time they ever got to know each other at that time was "4ever".)
Edit: Oh, and Drew's hometown is the setting of the Deoxys movie.
I'm waiting until Dogasu does the comparison, but the current vibe is "yes, it was a reference to the second movie." So, yeah, go with that, until you hear otherwise.
Suicune is different, yes, as "Don't Touch" had that dramatic irony. However, in Eusine's in-series episode, Ash said he met Suicune. Yet, he and the episode didn't say on either the events of "Don't Touch" or the fourth movie, which aired prior. That always bugged me, in the past. It's bugging me further in recent times, as Mew is now proving how Legendaries aren't always one of a kind (or has that changed when I wasn't looking?).
As for the first movie, I did forget that, as that's the most tight of all the movie allusions (so far). Problem is, it's been so long since it was last mentioned or Mewtwo had an actual appearance (S. Melody doesn't count), so one tends to forget about it.
And, yes, on Drew's hometown, but when was the information of his hometown dropped, anyhow? Which episode was it? I can't seem to recall. Oh, well, that's the way it goes.