As far the example is concerned I'd go with should have because you're finishing the sentence with "...I wonder why it's late". Should have is more used when talking about time and/or commands. It's usually said in a negative tone. "You should have done your chores", "you should have stopped for groceries", "you should have listened to me". Could have is more for opportunities. "He could have saved the files" "She could have called me for once". "I could have done more today". Don't worry too much about them because they are both really flexible for situations

could = possibility should = expectation If it's late, then you are talking expectation, so SHOULD.

Should have. Could have only really makes sense if you are placing the blame somewhere e.g. "The plan could have arrived by now if it wasn't for the bad weather."