See Using LMIC_setClockError on MCCI LMIC [HowTo] for notes about LMIC_ENABLE_arbitrary_clock_error and differences between SFs.
To debug you’ll need to keep an eye on everything: SF, maybe even on the frequencies that work/don’t work, and which of the gateway(s) that received the Join Request is selected to transmit the Join Accept and which work and which don’t. (But you’ll need access to the gateways to see that.)
For OTAA, that’s an error. It should only be configured for ABP in EU868. It will probably only affect joins on SF12 though, if anything at all.