he keeps saying my sister is hot but then he'll also say "I'm joking"
Does this happen way too often? Our gut doesn't lie, you know. If he has joked about it once or twice casually, I guess you've nothing to worry about. But if you sensed a tiny hint of truth to it, trust your instincts!
it's happened twice
You need to judge by his tone. Maybe he does like you but finds your sister attractive. Doesn't necessarily mean that he doesn't like you