I am guessing this is a bug because all my students have experienced this regardless of the colors they were using in their designs (we were working in PMS). Is there any rationale for Cyan having to be removed manually when deleting unused swatches in InDesign? Is there anything else outside of the design area using it?
Here's my guess: this could be due to paragraph shading feature (which has been introduced in CC2015 version, explaining why CS6 isn't affected by this issue).
Default paragraph shading color is... C100M0Y0K0 :-/
It seems to be part of the in-built indd prefs and that there's no way to change it...
Edit: in order to confirm my guess, I did google it, and found this interesting thread:
Looks like a confirmation.