There's a fairly easy example of how this can go bad here on earth. Cats and dogs don't innately hate each other, but everyone knows how they get on.

The problem is that cats and dogs have opposing body language; when a dog acts excited and happy, the cat interprets that language as aggression. For example, a cat with its ears down and tail wagging is a cat that's about to fight. A dog doing the same thing is being submissive.

Of course, this all assumes that any intelligent extra-terrestrial life even has any sort of body language or capability to communicate that we can even recognize.