Quality should be the biggest factor when it comes to selecting a roofer for your repair. If, however, you suspect that there are issues with the work, have a third party perform an inspection of your roof.
If they identify any problems with the job, make sure to document the issue with details and pictures. Next, review the contract or proposal that you signed to determine if this should be fixed by the roofing company. Call the contractor to inform them of the problem. A reputable company will send someone out to assess the work that was done and identify the cause of the issue. If you receive no response or help from the contractor, consult the Better Business Bureau to determine what steps you should take. As a last resort, you can take legal action to oblige the company to fulfill the terms of the contract.