you seem to discard the possibility there might be a problem in your gerbers or design
I recently had an issue where later designs of a board, one where I used discrete components instead of a daughterboard, did not work. It was a PCB to switch between other components using I2C. I checked with my scope and signals were getting through. For previous designs, I had shortened the cables and fitted my own 2.54mm Molex connector on the ends. Lately, I had decided to use the standard supplied cable even though it was a little too long because I didn't want to take my time up just crimping cables. None of the boards worked at all. I wondered whether I had made the right design for the discrete components, whether the extra length on the cable was affecting the signals or something else. I tried various values for pull-up resistors and some other changes but to no avail. I even considered manufacturing errors but there were no shorts and all signal paths were good. On the plus side, after many hours staring at a scope, I now have very good signal integrity
It took me a little while (too long) to realise that I had made two mistakes. One, I had swapped SDA and SCL on the board design, but the second mistake was I had done the same with the cables I had adjusted...
There was much self-chastisement and gnashing of teeth.
What are your design rules?
Personally, I make sure all my boards use the design rules supplied by JLCPCB for exactly this reason. I also make sure that if there are any holes for pins that they are oversized by the manufacturing tolerances plus a very little bit.
Maybe it was something in my specs that didn't get along with JLC's tolerances, but I was never given any warnings of the sort when I made the orders.
Well, unless you supply your specs to JLCPCB and ask them to check your specs against their tolerances (and pay them to do so) then, of course, they won't warn you about a problem they can't possibly predict.
They will just make the boards according to your gerbers, to within their stated tolerances, and any design problems that arise are beyond their control.
Of course, if the boards you received are out of their stated tolerances then you have a good case for getting a refund or replacement.
Are the boards you received out of their tolerance ranges?