This phrase means "I don't like that kind of situation."

A: I forgot my cell phone at home this morning.

B: Oh no. I hate it when that happens!

The word "hate" in English is perhaps not as negative as it might seem in other languages. In the example above, the speaker can say "I hate when that happens!" while smiling and laughing. Especially among younger people, saying "I hate ___" is common when talking about anything that they don't like very much.

You can talk about any situation with "I hate it when ___." For example:

I hate it when you send someone a text message and they don't respond for a day or two.