Try going to Patches>Relax>Curvilinear or Linear and relax the patches. Both of these functions should resolve any overlapping/twisting patch regions you may have and depding on your situation use either Curvilinear or Linear to relax.
The Linear Relax Patches operation relaxes all patches based on the position of their endpoints. For example, if a patch is curved, the operation causes the patch edge to straighten between its two endpoints. Because you can apply the Relax Patches operation more than once, individual patches can become increasingly straight.