It sure does contradict itself. That's why having a Canon or Not Canon section on pages is the only thing that's actually needed. If it contradicts animation, then it's Not Canon. Pretty simple. And as for Batman and Harley Quinn and Justice League VS Fatal Five, Bruce Timm has literally confirmed these to be canon within the DCAU so there's no reason they should be treated as any less on this wikia.
You just pick and choose what you personally consider canon to the universe. You don't like it? Not canon. Unfortunately whether you're into Harry Potter, Star Trek or Star Wars, every franchise has stuff that's not at the same standard as the rest of the stuff but that doesn't mean it doesn't exist in-world