"Wait up" is something you say when you are asking someone to wait for you, usually when you're going somewhere else; it's not really the best way to ask someone to stop doing something. You could potentially say "Wait!" to get them to stop temporarily, but it doesn't mean the same thing as "Stop" or "Hold up." If I wanted someone to stop doing something and I said "Wait!" I'd probably feel obliged to follow it up with "Stop!" or "Don't do that yet."