Only in AutoTune mode or in other flight modes? FYI, AT is partially active even in other flight modes.
I assume this is not a Nano (which has a slower CPU). Do you have extra features running (besides AT)? INS13? GPS?
I2C aux mags can cause issues (many do not communicate cleanly without extra pullups). Do you have an I2C mag?
What is the CPU usage while it is happening? Do you have more info on the warning? Are there any other system health issues?
I would consider increasing the telemetry data rate / air rate, at least for a test. If it still happens, I would completely remove AutoTune and see if it goes away. (Remove AT from FMS. Disable AT in System -> Settings -> HwSettings -> Modules if you enabled it there.)