Nearly all have reduced the number of belt loops to 5, so I always add 2 more in the back on either side.
I've started seeing really short zippers, which is unfixable and best to avoid.
I've noticed a lot of ill fitting jeans bunch around the crotch or suffer from being a "cheap hotel". Also unfixable.
Most are not lined inside around the waist and pockets.
Sometimes the pocket hole is cut too high, making it awkward to put your hand in the pocket. Or worse, theres not enough give on the pocket to fit your hand in.
Buttons and buttonholes don't always match well, especially on a button fly. I think it's easier to enlarge the holes, but sometimes the buttons can be oddly small.
And of course measurements are unreliable, but that's true of all clothes.
These are nitpicky things, but I notice them all the time at all price ranges. I expect they're decisions made out of carelessness, or to save costs, or because that was the intend result. Cynically, I believe carelessness is the most common cause.