Ali,
I checked your design, it seems you break the 5 mil spacing between via and tracks multiple places?
When I run the DRC checker that I have adjusted for JLCPCB rules, I get 1533 errors and 4 warnings...
673 is clearance warnings, 173 silk to solder mask clearance and 55 board clearance errors (and some minor ones)
My bet is that there are so much wrong that they flag the board even though you use the same hole and via sizes as I do.
I have just submitted a new design with the same sizes in again (this is the 4th design I'm doing now with the i.MXRT106x using these VIA's) it was reviewed by JLC, approved, I payed for it, and the are now in production.
Sorry, I'm not going to supply order numbers or such.
Hope you find a solution (or another PCB producer, maybe that is easier just to do that, find some that can handle the higher requirements)