So, I made a 3D picture of a cute mouse using Microsoft Paint 3D and exported it as a .3mf.
Why didn't the colors match when I opened the file in Microsoft 3D Builder?
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If you are looking at gross color defects, I would look a the raw codes generated in the 3mf to make sure they make sense.
If you are talking about subtle color differences, that is much more complicated.
Color have always been a tough thing to define as it is affected by whether the it is emissive (like displayed on a screen) or reflective (like a physical object). The way it is perceived is affected by ambient light, surface texture and more. I worked on a project once where Marketing wanted all the colors to match (on the screen, on paper, on plastic, on on fabric) and it was a mess.