Good Point.
I doubt it would be quite unsanitary to re-use the cup. If this is a one day thing, they most likely had no adequate portion control procedure. Maybe they had multiple cups for different types of coffee... (ie. Double/Double, Cream, Sugar, Black, etc.), and if they didn't mix the types and changed the cup frequently, I bet they could have pulled it off.

Or did you consider that maybe it was an error, and a staff member read the display screen and put it in a paper cup not realizing it was an "earth day coffee"? This could have been operator error.

Since it was the manager that served you, you should have asked her at the time. However you have a valid complaint based on your observation.

And you made me hungry for some Timmies!! :)
I wish we had some here where I am now in Michigan.
And is it just me or have the holes been constantly increasing in size?