LittleStain - The capx is too large, but I will be releasing a demo hopefully within a few days here.
— - They set themselves invisible. I know this because a couple of the objects are enemies that shoot other objects based on image points, and the enemies are still shooting objects at the correct location while being invisible (and also take damage).
Paradox - Also, if this were the case, it would be happening everytime.
Thanks for the responses guys - I'm incredibly confused. Half the time I test my game everything is fine and dandy.