It is difficult to tell what this “rough spot” is. Your doctor may be referring to dry patches on the surface of the cornea in which case you need to continue copious amounts of lubrication with preservative free artificial tears. The dryness may resolve with proper treatment. Another possibility is that you have a corneal abrasion that should resolve with antibiotics, steroids, and artificial tears. I would recommend that you continue to be closely monitored by your surgeon.
Hard to say what is going on. Did the doctor call it a "rough spot". Sometimes the surface cells will shift or there will be a scratch (abrasion) which generally heals or if the cells form a ridge, they may need to be smoothed out. Did they put a contact lens on your eye right after surgery? Do you have diabetes (more prone to epithelial slide). Are you over 40 (more common to have slide as well). It is possible that the flap has shifted, this can be serious. Another possibility is dry eyes. Are you seeing your surgeon or another doctor after surgery? If it does not improve soon, and your surgeon doesn't have a plan to resolve the issue, it would be prudent to get a second opinion.