Can employer take money from independent contractor check or withheld check.

An independent contractor is not an employee, so different rules apply. An independent contractor's pay is governed by the contract, or agreement, between him/her and the company he/she is working for. IF that agreement--whether written or oral (unwritten; also incorrectly but commonly called "verbal") states that the company may withhold money from the contractor to offset any balances due from the contractor this is legal--but if the agreement does not so provide that or contain that understanding, they may not withhold pay for a balance due. If you believe that they are violating the terms of the agreement under which you worked for them, you could sue them (e.g. in small claims court, for breach of contract) for the money.
If you should (i.e. actually are) an employee not an independent contractor, then not only can they not withhold your pay without your consent, but you may be entitled to benefits, to the employer paying the employer portion of medicare and social security, to overtime if you worked more than 40 hours, etc. The issue is not what they call you--it's whether in actuality, you are an employee. You can find criteria for when someone is an employee, not a contractor, on the U.S. Dept. of Labor website; in brief, if you only worked for them, if they set your hours and/or place or employment, or they told you how to do your job, you are most likely an employee. If you think you were misclassified, speak to the federal or your state department of labor about the situation and about what you may be entitled to.