Please clarify your question.
As a 1099 contractor, as noted above, you are not an employee. That means that the company technically has no say in when or how you perform your job.
Having said that, if you turn in let's say 8 hours, then that company must pay you for 8 hours. If the company is attempting to dictate that you must take an hour lunch, then the company is treading on thin ice between the lines of employee and independent contractor.
The issue here is as follows:
1) You can meet with the company and inform them that what they are doing is not correct
2) If you do meet with them, you need to be aware that they may terminate your "job" due to the fact that you are questioning their "policy", however, once again, you are not an employee.
3) You can meet with an attorney to get this resolved, but you will most likely face the same outcome as item 2 above.
4) You can switch "jobs"
5) You can continue working there knowing that what they are doing is not technically correct, but you enjoy the job and the pay.
Each state has labor laws that protect employees. They may specify things such as hourly wages, breaks, meals, and how to handle meals when the employee does not clock out for the meal. For example, at my employer, it is assumed that every employee working more than a certain shift will have a 30 minute meal break, and if they don’t clock out for the meal break, it is automatically deducted unless their manager performs an override.
However, if you are receiving a 1099-MISC form, then you are an independent contractor; you are classified as self-employed. You may work for one particular client but that client is not your employer. And, you are not covered by any of the legal protections offered to employees. Your relationship with your client is determined entirely by your contract. If your contract says that you will be paid a certain amount per day even if you work through meal times, then that is what you get.
It is also possible that your client has falsely categorized you as an independent contractor when you are actually an employee. Whether you are a contractor or employee depends on many factors including the financial relationship between you and the employer, the amount of control they have over your work hours and working conditions, and other factors.
If your duties and relationship are those of an employee, then by classifying you as a contractor, your employer is cheating you out of some taxes, and they are denying you many employee benefits that may be required by state law. There can be substantial penalties for an employer who mis-classifies their employees as contractors. You can file a form SS-8 with the IRS to have them review your situation. You may also have an avenue of complaint through your state labor board.