I think the game is seeing color kits as just another item in fusion so it reverts to the automatic level color.
ex.
Using a remove color kit on a power level 8 weapon
The weapon is normally red because thats the default for power level 8
If you fuse it with a remove color kit it shows that it will remove the color
but as soon as you actually fuse them the weapon reverts to the default power level 8 color instead of the level 1 color displayed when fusing them.

Its nothing major but it would be nice to have some customization options

That's as intended though as if you have no fused color it will automatically show the fusion level color of the item. Therefore if you remove the color kit it should default to the item level. I'd say the bug would be if it reverted back to level 1 grey when it was a highly fused item.

Sorry I was thinking that it was a kit that removed color from an item not a kit that removed other color kits...the name is slightly confusing.