Though from what I can guess, the problem is probably coming from these lines in "ExtraControllReadCode.asm"
Code:
notInAir:
LDA Object_h_speed_lo,x
ORA Object_h_speed_hi,x
BNE skipMainGameExtraInputControl
;;;; controller is not pressed
;;;; horizontal speed is zero.
;; check to see if in air, shooting, etc.
LDA gamepad
AND #%00100000 ; if down is pressed
BEQ notDucking
ChangeObjectState #$5, #$04
JMP skipMainGameExtraInputControl
notDucking:
LDA gamepad
AND #%11110000
BNE skipMainGameExtraInputControl
ChangeObjectState #$00, #$04
You could probably get away with commenting out this whole block of code (apart from the labels) and it'll be fine. IMPORTANT: Make sure you edit the right version of this asm file, there are three of them in the current version, and they each go to a different module.
As for WHY down is hardcoded into NESmaker, it's usually because the tool doesn't support that feature yet, and it's easier to just hardcode it in temporarily. At least I assume that's the case.