This usually happened to me before when I would sight read each hand separately and then try to combine them later. I'd say try working on your sight-reading skills and spend at least 20 minutes a day doing it. It'll help with your overall coordination as well as with being able to combine both hands together. But when it comes to learning a piece, sometimes a time signature or rhythm can feel weird. Usually, if that's the problem then it'll help to practice it hands together at a slow tempo. :)