May not be the same problem as discussed above, however, this morning I just noticed that the S Pen was "one click" out from the silo. Reading the discussions here prompted me to check out my S Pen settings, and that's when I noticed.
By "one click", I mean the position the pen is in after pressing on it once while the pen is fully inserted into the silo. I don't know how long the pen was in the "one click" position (still predominately in the silo), or when I may have unknowingly initiated a "one click".
"Advanced features\S Pen\When S Pen is left behind" is on, however, since the pen is still with the phone and in the silo in "one click" position, I don't expect a warning to occur. "Advanced features\S Pen\When S Pen is removed" is set to "Open Air Command", yet that does not appear. Perhaps the "one click" position qualifies as "fully inserted in silo", thus no warnings are triggered.
The above is with the One UI 4.0 update, unlocked model SM-N986U1; January 1, 2022 security patch.