Hello everyone, I am am writing a metal song in the natural minor scale in C. Most of the riffs are very lead based. I am using guitar pro to help me write it. The entire song fits perfectly within the natural minor scale aside from one note in the chorus. But something weird is happening with that note. I really like the note and it doesn't sound that bad too me at all. Here's the deal...

The natural minor scale I am using has the following notes: C, D, D#, F, G, G# and A#.

In guitar pro you can highlight certain areas of your song, then go to view, then to fret board. It will then pull a big guitar fret board up. From here you can highlight portions of your song, then click on the "scale" button with in the fret board that popped up. This will bring up a scales window. You can select the tone of your song and then tell it to find scales based on the sections you have highlighted. If I highlight the entire song guitar pro will tell me that the song is 100% in natural minor. However I have a note near the end of the chorus that is an A. A is not listed anywhere in the list of notes I am supposed to use to stick to the scale. I am aware that these rules are made to be broken and I am the writer, if I like it, then keep it. But I am wondering why I am being told it is fine when it's not in my list. Is there an unwritten rule that says it can be used? I don't really know theory yet.
Never seen a C scale without an E or B!

First, you need one of each of the 7 different notes in your regular major/minor scales.
If guitar pro told you that the C minor scale has a D#, A#, & G# in it then I wouldn't be surprised if it also tells you the entire thing is in C minor. Guitar pro or all guitar chords or whatever similar sites are not a good substitute for a firm grasp of theory, because they feed you BS all the time & if you don't know better then you take it all in.

Aside from that, you're putting entirely to much emphasis on the scale. It's not a set of notes that you have to stick to, but merely a set of tones that will generate a certain sound, which we describe as a song in a major key, but as you noted in the OP you like the sound of the A which is not a part of the scale. This doesn't make that note off limits per say, unless you want to stay true to the scale for some reason.

I always equate out of key notes to colors in paintings. Some artists like to create things just as they see them, like scenery paintings that look realistic. This could be thought of as using in key chords & notes from the scale, because it's what you are expected to use to make it look/sound natural. But some artists such as Picasso don't want to do what is natural or expected, which is what I equate out of key notes or chromatic or diminished patterns to do. It's the unexpected & unusual form to music.

It's all about what you wanna convey: normal, serene, calm, soothing; or wild, untamed, extraordinary.
I'm an

I'm Good at Math
If you want to explain it using scales, then if you're using A instead of Ab, then you can say that all of the notes fit into C Dorian, or, you can say it's a note borrowed from the C Major scale. Generally, the Guitar Pro scale finder is bloody awful, when I used to try it, it came out with 70% Hungarian Minor and 35% Superlocrian and what have you, it is much better to use your own theory knowledge to tell the key of something. However, as it's you who wrote it, really, you have the final say, what's the key signature? That's the key if you've done it right. Perhaps Guitar Pro has improved to detect the odd non-diatonic note? It's been years since I've had to use it, it's been updated so many times since then.
Lesson: don't expect anything or anyone to know more about your music than you do.