In season 1 episode 4 "Where No Man Has Gone Before", why is Spock clearly wearing a command uniform when he's a Science Officer? Also, why does he look like he has got deep space jaundice?
A piece of trivia states that because of the episode being the second pilot, the 'colors had not been finalized'.
The familiar colors and positions of the crew had not yet been finalized when this second pilot was shot. The tunics for operations crew are beige instead of red. The locations of the helmsman and navigator are reversed (when Kirk is facing the viewscreen, Mitchell, whom Kirk addresses as "helmsman," is on his right, and Kelso, the navigator, is on his left). Spock is wearing a gold command shirt, not a blue science one. Both Mitchell and Kelso wear beige operations shirts, rather than the gold command shirts later associated with their stations. Smith, the captain's yeoman, wears a gold command shirt, and Lieutenant Alden, the communications officer, wears a blue sciences shirt, rather than the operations shirts most later yeomen and communications officers would wear.
From: IMDB trivia
Where No Man Has Gone Before is the second pilot of Star Trek, produced before any of the other aired episodes apart from segments of The Menagerie, which contains parts of the original pilot, The Cage. Many details of the series had not been finalized, to wit: costumes and makeup.
Spock wearing command gold is not such a big oversight - while he was head of the science department, he was also the first officer: a command position.
This uniform style was only used for this episode and "The Cage", and Spock isn't the only character wearing the "wrong" color - note that Scott and Sulu are not in their "normal" colors either:
Spock's makeup style had not been finalized by this episode, either; the brows are a bit more severe, his complexion is more sallow, etc.
Note that Uhura also wore the "wrong" color in one episode:
There's no accepted in-universe, canon explanation for these differences AFAIK - you can handwave it away as people transferring to different divisions offscreen (for example, I think Sulu was in Astrophysics for WNMHGB) and Starfleet changing uniform styles in the span of a few months. And maybe Spock getting some time in front of a sun lamp.
But, honestly, it's not worth the effort to canonize these discontinuities. It's the reality of producing a weekly science-fiction television show that you're making up as you go along.
Speaking of this, it annoyed me when they felt they had to canonize the changes in Klingon appearance between TOS and TMP by introducing the stupid augment virus in ENT. They should have left it at Worf's "we don't like to talk about it" statement in DS9.
Real military and naval services change their uniforms from time to time. And when a uniform change is made it may take time for all members to replace their old style uniforms with new style uniforms. Thus for a period some may wear old style uniforms and others may wear new style uniforms. Someone who has both styles in his closet, locker, or whatever might sometimes be allowed to switch back and forth during the transition period to use the old style uniforms until they wear out.
As a general rule TV episodes can be viewed in order of production or in order of first broadcast date. Star Trek episodes can also be viewed in stardate order.
TOS episodes were broadcast by the NBC Network. The NBC executives would usually have a few completed episodes on hand to choose from. After filming the episodes would be completed in post production which took varying time because of more complex special effects in some episodes.
Thus completed episodes would not be delivered to NBC in chronological order of filming - or production order - but the much different completion order. And NBC executives did not decide to broadcast episodes in order of production, completion, or delivery to NBC, but in whatever order they thought might be best for the ratings.
Watching the first half season of Star Trek in production order shows the uniforms, props, sets, etc. gradually changing from those in the second pilot "Where No Man Has Gone Before" to those in most of the episodes. Watching the first half season of Star Trek in broadcast or original airdate order shows them zig zagging back and forth in the first few episodes.
So long as you watch in production order you can see uniforms gradually becoming more and more like those in most of the TOS episodes. if you watch in stardate order or airdate order you will seem the wearing of uniforms go back and forth between "Where No Man Has Gone Before" style and TOS style. In the latter case one can imagine that the crew members have both old and new style uniforms in their closets and are relatively free to choose which style to wear during a transition period.