For completeness, I've done some more work...
I checked fuse.rmp, it did not have the "-1" settings applied to anything.
Each game remap would have been created from the fuse.rmp (using the retroarch menus.)

I then checked all my game remap files. 13 of 28 files had this problem.

Next I tried to recreate using the retroarch controls menu.
Cycling right through the available options that can be mapped to the port 1 controls I have:

"---"
Up (1)
Fire (1)
Keyboard Overlay
Up (2)
Down
Left
Right
Fire (2)
Fire (3)
Enter
Space
Then back to "---"

The (1) etc are my addition, "Fire" appears 3 times, "up" twice.
I set some buttons to each of these values, wrote a game remap file and checked for "-1". None of these options generated the "-1".

Next I cleared the options on buttons A, L, L2, R, R2 & X (all originally set to differently) and bingo, I recreated the problem :

input_libretro_device_p1 = "257" input_libretro_device_p2 = "0" input_libretro_device_p3 = "259" input_libretro_device_p4 = "0" input_libretro_device_p5 = "0" input_player1_analog_dpad_mode = "1" input_player1_btn_a = "-1" input_player1_btn_l = "-1" input_player1_btn_l2 = "-1" input_player1_btn_r = "-1" input_player1_btn_r2 = "-1" input_player1_btn_x = "-1" input_player2_analog_dpad_mode = "0" input_player3_analog_dpad_mode = "0" input_player4_analog_dpad_mode = "0" input_player5_analog_dpad_mode = "0"

There appears to be a bug. When clearing a mapping using the retroarch "Controls/ port X Controls" menu from any value to "---" the resulting remap file contains "-1" for that key and this stops you mapping the button using the Retroarch "Options" menu.

I hope this helps repay the debt a little!

Is there a menu option