When Minecraft generate a Custom Potion with multple effect, the color of each color is merged to create a unique color for the custom potion.

Example:

/give @p minecraft:potion 1 0 {Potion:"minecraft:water",CustomPotionEffects:[{Id:3},{Id:6}]}

ID 3 is yellow, ID 6 is red, the result is an orange potion.

This also work with effects added to real potion, example:

/give @p minecraft:potion 1 0 {Potion:"minecraft:fire_resistance",CustomPotionEffects:[{Id:6}]}

fire_resistance is orange, ID 6 is red, the result is a dark orange potion.

But with empty potion (uncraftable potion), the effects colors are ignore, and the color is forced to pink:

/give @p minecraft:potion 1 0 {Potion:"minecraft:empty",CustomPotionEffects:[{Id:6}]}

empty is pink, ID 6 is red, the result is ... pink, the effect color is ignored.

The normal behavior should be the ignore the empty potion color, the pink color should apply only when there are no effect, when there are effect the empty potion should work like the water potion: only the effect color are used.

For now the only solution is to use the "water" potion as base for custom potions... but the name of water potion is "Water Potion", I think "Uncraftable Potion" (name for empty potion) is a more correct name for potion that are not craftable.

Because of this bug, map maker need to add unneeded NBT tags like CustomPotionColor or display/Name to have a valid potion.