You feel it grinding while manually turning the stepper shaft
The M3 bolts might loose due to the elasticity of nylon spacers in the long run, especially in a heated environment. The stepper armature might grind surrounding magnets.
Replace the nylon washers with M3 bolts and M4 nuts as washers (or an equivalent) as shown in the pictures.
For a temporary workaround, just check and fasten the long M3 bolts before you have time replacing the nylon washers.
Remember to calibrate again.
M3 nuts (x4)
M4 nuts (x4) or 3x6x1 metal washer (x8) as spacers
Loctite 243 thread locker