I was wondering if I could add more rows to the palettes, as 3 colors seems pretty limited. If so, how could I? Thanks in advance.

You can resize the sprite in GameMaker and add more colors.

I know, but when I tried to resize it, some of the other colors got confused for white.

Make sure you're following the correct palette format. The first column is the sprite colors, while the other columns are the in-game colors. https://platformfighterengine.github.io/#/tutorialB6

I know, I did that, the only difference was that the first and second collumns were the same.

Can you post an example image of other colors getting confused for white, with the palette & sprites used?

That's weird, I can no longer produce the bug, I found a short-term solution, and now it's completely gone. I promise I'm not trolling, I'll find a picture if this happens again.

It happened again. I am on the second skin and it doesn't work.   First picture is palette, second is in editor, third is in game, sorry about format.

Make sure that the color hex codes match exactly. If the issue is hard to recreate it could also be a caching issue, in which case you should Clean the project with the brush icon at the top.