Unless its totally closing off all blood flow to his boy parts, it won't cause future problems.
Also, you shouldn't wear bulky winter clothing in the car seat. I live in Minnesota, I know cold winters, but you never wear bulky clothing in the car seat. Read it in the car seat manual, it will say the same thing. Basically what happens in a crash is there is 3000+lbs of force put upon everything, and that puffy winter jacket will compress and that will make the car seat harness too loose, leaving your kid to be ejected or throw around violently.
If you doubt, try this. Put your child in the car seat with the jacket on, and buckle the car seat harness, and tighten it so you think its safe. Then, unbuckle and remove your child wihtout loosening the harness, and remove your childs jacket and rebuckle her into the car seat. All that slack in teh belt is what the harness would look like in a crash when the jacket compresses. If you sit on the jacket and it compresses, then imagine thousands of pounds of force on it in a crash.
A polar fleece is warmer than a puffy jacket and its car seat safe.