Diapers are stained. Like, HELLA stained. They don't smell but hoo-boy that is bright. Breastfed poop is bilirubin-heavy so it stains everything it touches. It doesn't mean it's not clean, it's just going to show up. It fades as you wash more but if it bothers you, dry it in the sun. Some brands are also more prone to staining (looking at you Grovia snap-in inserts) but it does not affect their function whatsoever.
Diaper cream. Zinc-based diaper cream may leave behind white stains. You can try a decreaser (dawn dish soap) and some elbow grease, but they should fade over time with continued washes. Again, this should not affect their function.