can a employer take money out of your payroll check for money missing?

Alright so i worked at a pizza delivery place. and we had a cash box in which we made change for people. so lets say a pizza cost 24.99, i would make change for a 40, and after the delivery i would get 43-45 bucks that 3-5 dollars is my tip., now i went into work and he said 50 dollars was missing out of the cash box. twice, and he took it out of my check, and i only got a 23 dollar check. but i am pretty sure i did not go home with 50 dollars in tips twice. and also to that note is he doesn’t keep records on the cash boxes. and when i confronted him about it all i herd was a whole lot of bullshit. and i cant do a damn thing about it i don’t have 5 thousand dollars for a lawyer. what should i do?.
also i worked about 15 hours and on my check stub it said 3.something. can you manipulate checks or is that another illegal l thing that he did.?