It is hard to tell what the condition is for one of your notches. Look really close at them. Do they look the same or is the drooping side worn ever so slightly?
Here is one of your pictures depicting the gap highlighted
purple for exaggeration.
Your notch for that side is the problem in question.
If it's not the notch, a suspected problem stems from the rubber legs of the cover seated inside the bottom case. When you slide the cover in and out, something catches and pushes the cover outward and makes it bow up.
Edit - stupid BB color code messing up this post.
if they arent latching on correctly would there be a fix for that?
There's two ways to fix this. Either replace the cover piece or use a thin strip of double sided tape. The tape method is temporary where you have to do upkeep in replacing the strips.
Edit #2 - You could also try mounting pad/foam as a column in between the areas where the SD card and game cart. Also temporary.
