I am a member of the State Bar of California, the U.S. District Court for the Central District of California (LA/OC Metro, and surrounding counties), and the California and National Associations of Realtors. Please permit me to assist.
First, the fundamental rule of California employment law is that an employer can terminate an employee "at will:" at any time, for any reason, or for no reason at all. Cal. Labor Code Section 2922. Because of this, the employer can simply say, "you're fired," whether or not you sign the warning and whether or not you are clocking in correctly.
There are, of course, many exceptions to the rule stated in Section 2922 (discrimination based on race, color, nationality, religion, sex, age and disability; jury duty, complaint to a government agency about employer violations of law, etc.). However, I don't see any of the exceptions as applies to your stated facts.
Concerning whether or not your being required to clock in, given your status as a salary-exempt employee, you may have a claim for treatment as an hourly employee, which may permit you to obtain overtime hours. In order to evaluate this, I would need to know all of the facts about your employment, and I would need to review all of your personnel and payroll records -- something that cannot happen in this forum. And, in fact, if you could prove this, then you could complain to the Labor Commissioner, which would immunize you from retaliation and prevent your employment termination. Cal. Labor Code 1198.5.
As to whether or not it's a good idea to sign the written warning, you can sign, and write above your signature that you dispute the claim that you are in willful or negligent violation of any employer rule (which can be used to protect yourself from being denied unemployment insurance benefits, if you are terminated). And, you can also refuse to sign, which will make it impossible for your employer to prove that you were warned of your violation prior to termination (which may also protect you from losing your right to unemployment insurance benefits). On balance, it's probably better to sign, and write in your dispute on the form.
But, unless you actually file a wage claim with the Labor Commissioner, or provide a written complaint to your employer's HR department or to a member of executive management before you are terminated from employment, then you cannot use retaliation as grounds to protect yourself, because the employer will not have retaliated.
And, if you choose to write to executive management, then you will need to prove that your complaint was made, because, in my experience, employee complaints that could operate as grounds for legal action against an employer have a tendency to vanish mysteriously, and employers frequently deny ever receiving any such written complaint.
That said, if you are interested in having a lawyer assist you in protecting your rights, I will send you a premium services offer, and we can take this matter offline.
If not, then I hope I've answered your question. Please let me know if you require further clarification. And, please provide a positive feedback rating for my answer (click 3, 4 or 5 stars) -- otherwise, I receive nothing for my efforts in your behalf.
Thanks again for using Justanswer!