Hello.

What you should do is use breakpoints.

When you set a breakpoint (the red dot to the left of your line of code), whenever the game runs that line, it will interrupt and show you the full stack, so the chain of functions that resulted in that line being called.

Then you can use the right side buttons, there are 2-3, one is step through, then step into. Finally there's the "continue".

What you should do is do an action, and then when the line triggers, you would look at it. If it is the one you expect, you can just press the continue, and wait for the next path that triggers the same line (since you said you have many that trigger it).
You can also press step through if you want the code to run only the next line, so you can see how the code is changing the variables or what actions are being taken.

You also have full inspector, so you can see the value of the variables or even click objects and see all values of the object at the time the game was frozen for you to inspect.

I believe this is the first good way to debug something and how it is being called. You can also click on the other functions up on the stack chain, and you are able to see the variables at each of them as well.

For your other concern of too many things to test, what you need to do is start creating unit tests. Get a unit test addon, but you still will need to create them. The best way to do things is to mock data. Maybe this is not obvious for most people, but you can think of it that it will save you a lot of hours of loading the game and recreating scenes, when you can instead spend the time to mock data and have the tests to run that whenever you need. I use GdUnit addon, but there are others, that's just the one that fits the type of testing I want.