Can my employer withhold a weeks pay because my paperwork wasn’t turned in on time?

It depends on the type of paperwork that you are referring to. If it was documentation relating to the processing of payroll, then yes, a delay in your recieving your wages was reasonable. However, it is not a reason to withold 2 weeks pay indefinitely. Additionally, if the paperwork in question had nothing to do with payroll matters, then witholding your wages (for any length of time) without your express written consent was illegal. You can file a claim with your state's department of labor and or sue or employer in small claims court (although that could potentially lead to your termination). 

What paperwork? 
If you mean a time sheet or other paperwork required to process the payroll, then because you did not provide what was needed, they can withhold the pay until you do provide it. Payroll often cannot be processsed without certain information from an employee; and payroll is a process, with certan deadlines--it must be completed by a certain time or date to get out on time, so anyone who doesn't hit that deadline will miss that payroll.
(As a practical matter, they will catch you up next payroll, if you provide the information before then.) 
If you mean information unrelated to your payroll (like some other paperwork they like to get), then no--they can't delay your pay for that (but could discripline, or even terminate, you).