In-between He-Man's season one and season two something happened to Kothos.

Kothos was by no means a big recurring star in the He-Man series, although he was part of the "Wizard Trilogy" as we like to mockingly call it; "Wizard of Stone Mountain," "The Witch and The Warrior" and "Revenge is Never Sweet" are all linked by two characters; Kothos and Malik. Kothos did have two memorable appearances and on both occasions managed to bring out some of the best character writing in Evil-Lyn. There was one strange thing between Kothos' first appearance in "The Witch and The Warrior" and "Revenge is Never Sweet," his look changed considerably. Usually if a character makes a second appearance in the He-Man or She-Ra series, they are fairly close to what they looked like before. Kothos didn't fair so well.

MU59 - "The Witch and The Warrior"
Here is the first time we see Kothos. The character has a lot of blue in his costume, and his skin is of a very dark tone. By the end of the episode Evil-Lyn transforms him into a giant blue sand-slug, and that is the last we see of him.

MU102 - Revenge is Never Sweet
When Kothos' reappears as a sand-slug in this season two episode, his blue skin has now become a dark brown, more fitting with the sand environment, and that of the many desert creatures that dwell on Eternia. When Orko makes the very strange decision to transform his old enemy back to his human form, we expect the original Kothos. Instead we see a very differently colored version! Whereas the original Kothos dressed in many shades of blue, this one looks more regal in red and white. One of the strangest differences is that Kothos' skin tone became much lighter.

Why these changes were made is unknown, but they can't just be casually ignored.