For example, how Crookshanks keeps attacking Scabbers, and it looks just like a cat/rat thing.

Hermione's time travelling ability is somewhat less subtle, but since I didn't catch it the first time, I shouldn't criticise it too much.

As red herrings go, there is the half-hearted one of Snape trying to kill Lupin. And the other one which is barely starting at this point, but which appears to be building Lupin as a baddie. Neither are proper red herrings, I think, but they seem to have been planted to make the reader (or at least me) think that they (*cough* I) have spotted the real red herring, which makes them stop looking for another (ie. Sirius).

We get indications that something is wrong with Lupin, anyway. And that Snape is worried about it or has a stake in it. And of course the very pointed introduction of werewolves.

Grindylows are introduced. And Harry is told how to fight them.

One of my favourite parts (in terms of rereads) of the book also shows up: when Sirius Black tries to break in to the Gryffindor Common Room. It had quite a thrilling effect the first time I read it (and reading it now recalls that), but when I read it now the emphasis is on Sirius' worry that Harry is in danger from Pettigrew. I like how the fact that he broke in on Halloween, when nobody would be there, is construed as a mistake when it is clearly a clever time.


In themes:

The theme of trandformation is becoming apparent. It is one of the central ones of the book, and tied to that of double or wrong identity (ie Sirius apparent Death Eater, Pettigrew apparent rat, Werewolves apparently bad, but Lupin not)