Marlin firmware question for dual extruder
There is nothing to worry about, this is a feature not a bug.

Extruder refers to the active extruder, the loaded/active tool. Based on the active extruder the Extruder controls either your Extruder E1 (this is known in the firmware as Extruder E0!) or your Extruder E2 (the Extruder E1 from the firmware).