If Cal's existance is basically just a circle that just starts over and over again, does that mean that there could be multiple Caliborns/Gamzees/Equiuses inside that puppet??? Or am I missing something, cuz that don't exactly sound right...

Lil Cal’s timeline splits during the Scratch so there are two Lil’ Cals at the same time and the souls can’t go into both so they go into one and the other one is empty.  The one with the souls has it’s eyes ripped out and is probably destroyed and the one without them get the souls put in by Dirk.