I asked this question once again on the Don Bluth Films Facebook page, and this was their response:

Quote

Good catch. You are absolutely correct. Yes, it was "sort of" intentional. And no, there were no potions involved.
  Warren T is a runt cat, smaller than the cats but larger than the adult mice, not by much. The idea was that he was the bully of the cats. A little guy with a huge ego and a bullying attitude, sometimes referred to as a Napolean complex. And, with his small size and a crude disguise, he could pass himself off as a rat and a "friend", offering to help new-comers to America, get a job. Tiger on the other hand was a huge cat, two to three times as big as the cat gang members, and literally towered over Fievel.
Many times, trying to stage the various character sizes, like Warren T. with Fievel vs, Papa with Fievel, together within their environment meant we took some liberties or artistic license to avoid cutting off parts of their image on screen and give the shot a believable and pleasant appearance, without having to draw tiny minute images of Fievel.
Actually, as far back as I can remember, we've never had a viewer write to us about the discrepancy in the Warren T's size. We thought that some in the audience might have brought up the size changes on Tiger during the "A Duo" song performance. Which, was a much more radical discrepancy. But, no one did.
  Again, good catch and thank you for asking about it.

Hey, ARAJediMaster, I refuse to watch those videos. And Ace is exactly right. The new film is excellent while the prequels were terrible. Deal with it. You have no right to try to dampen anyone's enjoyment of this film, regardless of how butthurt you are. The only documentary I am willing to listen to regarding the prequels are the Red Letter Media ones.

Ducky in the beginning stages of becoming a ninja turtle