No difference but the first is more usual. He wasn’t expected to return until three o’clock.

The sentences are logically different. The situation becomes complicated because "expected" and "not expected" are not quite the opposites they seem to be. "Expected" can mean "likely" and it can also mean "required". "Not expected" can mean "surprising" and it can also mean "not required". So far, so good. Things get interesting though when you compare likeliness with unlikeliness. They are less related than you might think. If I tell you that it is likely (say, more than 90% probability) that he will return before 3:00, the opposite statement would not be that it is unlikely that he will return before 3:00. Rather, the opposite would be that the probability would be less than 90%. It could be 80% which is STILL likely. For that reason, your two sentences should not be directly compared.