How long has it been since the paint was applied? It should blend together after the paint has cured, 2-4 weeks depending on temperatures and humidity. As noted there are 2 different application methods, paint is thicker with a roller than a brush. Color can also have some affect on the sheen and the way the paint dries. Other possible causes are the number of coats and time between each coat.
Give it time to fully cure. If there is still a problem call the store were purchased and talk to a sales person, could be a bad batch of paint.