Do you mean like a big orange stain where there was poop? If so, then this is totally normal (and would happen on clothing too, not just diapers). Breastfed baby poop stains are very bright, almost neon-like sometimes! It doesn't really matter that the poop wasn't bright orange or yellow, that's just the color that it leaves behind. I know you say it was a faint spot so maybe your wash routine is pretty good at removing most of the stain but there's just a little left behind... I can't see how you would have noticed this with disposables though, it's not fabric so may not stain the same and it would be hard to see it anyway considering it's covered in poop when you throw it out...
As long as it comes out easily in the sun then I'm 99% sure this is what it is and it's totally normal. On the other hand, if it's a very small spot (like smaller than a quarter for example) and it doesn't come out with sunning, then that's a different story.