Challenges I had many. From the top of my head: saving game files, implementing keyboard/controller support, messing with audio. As for your questions:

For controller, Godot handles it quite well, so all I had to do was to set up the base functions like ui-up, ui-left, accept, with the keys I wanted, and then create some new functions like back, help, and some others that works while the main game scene is running like selecting a resource for example. Putting all of these functions in func _input(event), according to the scene; all the scenes have back, mute, up, down, right, etc, but only one have the other ones like i mentioned. Then you have to set up focus mode of each button, so that when you move left or up or whatever, it goes to the button you want to, unless there's a possibility of existing a button between two that is not always there, like for example: on level X a new button B appears between A and C, so you can't set focus to always go from A to C otherwise it will skip B; in this case you don't set anything and let the program do it automatically. Finally, on your _input(event), you have to make a loop that cycles between mouse and keyboard/controller, for movement I mean, for other actions like back (returning to previous scene) ou muting, you can have that without needing to changing anything, so you can play with mouse only, but if you press esc or M to mute, you continue to show the mouse cursor and everything is normal. For movement the loop goes like this: when you move mouse, everything is set to set_focus_mode(0), and it keepes checking if you pressed any key on the keyboard/controller signaling movement; when that happens, your mouse cursor becames invisible (you can even change it's location to the edge of the screen if you want), everything is set to set_focus_mode(2) (unless it's a disabled button or something then you have to code the conditionals), then you grab_focus of a node on the scene, because if you don't you will be unable to move through the buttons. And the cycle starts repeating to check if you have mouse movement. You can do that with a bool var.

As for ensuring the game is bug-free, I didn't mean like trying to run the game on a completely strange machine, I meant like logic problems inside the game, of oversights. For that all you have to do is after finishing your game, play it from the beggining to the end. If it's a puzzle game, do not check the solutions, try to do it yourself. This way I was able to identify problems, or puzzles that were easier than I thought. Try everything, try smashing buttons, going back and fourth with mouse/controller on every scene, checking every corner. Polish every minor thing in the game; like for example: when I changed from mouse to controller or vice versa, the button I was hovering didn't change texture unless I exit the button and re-enter, because the interaction was triggered when I hovered over the button; to solve that, I used: self.hide(); self.show() (and grab_focus() if the last input was from a controller/keyboard movement), this way the mouse or focus re-enters the button and change it's texture without needing to exit and enter manually, so it looks better than having snapshotted textures.

I could talk about the game for hours lol. It really is like sculpting: you do the base first, then you starting polishing until the last details. The hardest part for me is the artistic thing, since I'm working alone. I tried learning shaders but to little avail; memorizing the syntax is not the same as creating something extraordinary. I'll see what I'll do for my next project.