I suppose that's the good - and/or bad, depending on your viewpoint - thing about DW; unlike other shows it doesn't have a "bible" and there's no universally agreed canon. Most people tend to say that "what's on telly is canon" and the books, audios etc. are non-canonical spin offs. Others argue that canon in DW is whatever you want it to be, so you can keep the stuff you like and jettison the stuff you don't. It's frustrating when you're used to shows that DO have an established canon in the way that DW doesn't.

That doesn't mean I can excuse some of these inconsistencies though. To have the Doctor and River meeting strictly in reverse order seems far too contrived (I'd made the same assumption as you) - which is why I'm now wondering if it's because there's someone/something else dictating the course of events which could certainly tie in with the fact that we already know that River isn't all she seems to be.

ITA about the prison though. You'd have thought they'd have found a way to keep her locked up by now!