I agree with reporting them, and the fact you said "we only claim 10% of our cash sales" is concerning as well.
If your employer refused to correct things, you can fill out Form 4853 as part of your tax return and use the proper amounts that you received. Should should be able to type "4852" in the search box within the program.
https://www.irs.gov/pub/irs-pdf/f4852.pdf
