Is it legal for my supervisor to clock me out on breaks I did not take?

I think with this "undeniable" proof you possess you should contact the California Department of Fair Employment & Housing... and an Employment Attorney. This appears to be Criminal Fraud, and the local Sheriff's Department would like turn over a claim of Criminal Fraud to the District Attorney with your 'undeniable proof". JUST BE ABSOLUTELY CERTAIN this 'undeniable' proof really, truly cannot be challenged in any way (or your unemployed and likely denied Unemployment Insurance). The California Division of Industrial Relations www.dir.ca.gov has a Labor Board with which you can file for getting paid the missing time for those breaks... start there.

No. That is not legal. Feel free to contact me or another attorney. You have two years from the time that your employer started doing that to complain (3 years for willful violations of the Fair Labor Standards Act).

Business etiquette suggests that you take this up with your supervisor or HR first. If you don't get anywhere, you can complain to the Dept of Labor, Wage & Hour Division which has offices in most cities. Assuming you are an hourly employee who is eligible for overtime, this practice is effectively making you lose potential overtime and depending on your salary structure, your wages.

You may have the basis to file with the Department of Labor or speak to an wage and hour attorney over this issue.

Yes, you will want to contact the labor commissioner for an initial discussion.

Your short answer is yes. If you were supposed to take breaks and refused, you may be on weak ground. But, if you could not take those breaks because of work load, were not asked to take those breaks, or did not know about the breaks, an attorney could possibly help you recover monetary damages.