I’ve gotten 4 anti cubes, but only three of the are from the clock (I think). I know how to get the anti cubes, but now my clock only has ONE HAND... I don’t know what that means or what I should do...
If you've already collected three anti-cubes from the Clock Room, then the clock itself is correctly displaying only one hand - each one of the cubes you collect will cause its corresponding hand to briefly flash and disappear.
Check this YT video at (0:23) for a demonstration of this effect:
If you need a reference on which clock hand you still have active, this old Arqade question has a list of each hand and their estimated time cycle.