I have received and assembled a Framework Laptop 13 AMD AI 300 series. Upon completion I noticed that the middle part of the right side of the input cover doesn’t sit flush. I have tightened the fasteners. Is this expected? Is there a hardware problem?
That’s where your WiFi card is. I’ve had that happen before when I didn’t have the antenna cables tucked inside the case. Since there’s some slack on the cables, it’s easy for them to pop up onto the edge of the case.
Yep.
Yeah, those look fine to me. Sorry, that was my only theory 
.
Personally I would take a known flat edge to confirm the bend is in the input cover rather than the chassis. If it is the cover then flex it / bend it taking your time so it is flat again or even a little concave.
Be glad your bend is in an easy to remedy location, mine is between the ports and the hinge and I really struggle to get that bend out.