When cutting tenons, it’s easy to overcut a shoulder. To correct a small gap, assemble the joint, and then place a card scraper flat on the mortised piece. Using the metal as a spacer, score around the tenon with a knife. Now disassemble the joint and use a chisel or plane to pare up to your scored line.
When the joint’s reassembled, the shaving or two removed from the fat edge should allow the shoulder to sit seamlessly on the joining piece without affecting the fit of any other parts.