This message is a warning. It is not an error.
Illustrator presents this warning whenever you have spot color mixed with other color (CMYK or RGB). Even if everything is fine in the file.
What Illustrator is alerting you to is that there may be a change in colors if you used any transparency in the file and a spot color interacts with that transparency. Transparency constitutes anything with utilizes an opacity setting or a blend mode.
If you have no such interactions, then the warning is just a warning and you can ignore it.
This warning does not mean there is a problem with the file. It is just telling you to check the file. Illustrator can't check the file for you. All Illustrator knows is that there is transparency somewhere and there is a spot color somewhere in the file. Illustrator does not know if the spot color actually interacts with the transparency. The warning is not referencing any color usage, it's referencing transparency usage. You need to check that.
What happens when spot color interacts with transparency is that the output will use CMYK to blend the appearance colors. You can't place a 100C 50% transparent object on top of a solid pantone color and expect to retain the solid pantone color by default -- you would need to adjust knockouts or overprints.
An easy way to check transparency in any file is to
Select > All, then choose
Object > Flatten Transparency and tick the
Preview box. Look at what the preview does to the artwork (don't click OK, just look). Or use the Flattener Preview Panel (Window > Flattener Preview) to see where transparency is in the file. Those are the elements where transparency is a factor.
The file you linked to appears fine, although it is a 5 color piece of art (CMYK+1). But then, I'm not getting the warning with it either. So I think you may have removed something which may have been triggering the warning.