Oh this reminds me of when I was working on embedded Linux devices for vehicles.

We had a new batch of hardware come in that had a failure rate of about 50%. Normally it was on the order of < 1%. Our CM was very good at troubleshooting.

Nothing had changed in the BOM so we were left scratching our heads.

Hooked up the JTAG debugger to see where it was failing to start, and the CPU wasn't even coming up. Power rails looked good, but the CPU just wasn't booting.

Eventually we discovered that the supplier had given us a batch of crystals that were slightly more sensitive to the capacitance, and our design was just on the margin of working.

Lowering the caps to the proper values according to the xtal's datasheet got everything working again.