Color are fine
The layout and scene is awesome and you are doing great!!!
See this for my take
You must focus on color unification. The less colors you use the better it will look.
You now have over 256 because your tools and prefs in Photoshop are not correct.
All tools MUST be set to ZERO tolerance and no auro anti-alias. Hardcore opaque pixels.
Also make sure your lines are clean and isometric, you have been sloppy in places.
again...you are doing awesome.
ps: If you distrust your color sense for whatever reason use reference materials and other images.
If it looks right to you for your project then borrow them. There is no such thing as copyrighted color palettes. Don't let pixelartists and especially dollers to tell you otherwise.
Just in case I'm wrong I claim all the blues in the universe and nobody else may use them