I faced such a strange issue after applying the Unwrap command. As far as I can tell, the mesh geometry is fine here but somehow some of the UV's are not aligned as I expect them to be. You can see one of them in the image below, under the green rectangle. Does someone know how can I avoid this?
When you unwarp try change method from Angle Based(default) to Conformal or uncheck Fill Holes More About Unwarp Options