During a normal filament change cycle the printer will cut the filament at the head so it then can be pulled back to the spool via the AMS to change to another color.
During a filament runout situation, the filament will be pulled off the spool and is pulled via the extruder until the end reaches the filament runout sensor. This will trigger the AMS to load in the next filament to continue printing (with the same filament).
The problem arises when the filament has been pulled from the spool in the AMS but the program calls for a filament change to a different color. The AMS can’t pull the filament that is in the tube back and will error out.
In short, auto refill works well when you are printing one color, not when you are printing many colors.