I used to work for a family own pet store. The owner was always difficult. I'd have to wait days to receive my checks instead of on payday. She would be constantly taking money out for ridiculous things. For example if an animal died she'd take it out of my check, blaming me for the death. A lot of it was total nonsense and eventually why i quit once i found another place of employment.
The better place to start with would be your local state labor agency because it sounds as if there were a lot more workplace violations than just overwithholding on tax.
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Good afternoon. Your issues are greater than just the tax implications you mention. While you don't want to pay taxes on unearned wages, you are entitled to be paid for the time you worked. You should speak with an attorney specializing in employment law/unpaid wages. Before your meeting, be sure to document every instance where your employer arbitrarily withheld money from your paycheck or failed to fully compensate you for the wages you earned. Remember: your wages are your property, not your employers'. Best of luck!