Weird palette choices

[Dolphman]

Ditto on Bowser's green body. Luckily, it was fixed in the GBA port.

As a DOS game player, PCs at the time had three well known graphic formats known as CGA, EGA, and VGA.

This is CGA:
 
Looks like the inside of a migraine, doesn't it?


Here's EGA:


It was used in some great games, such as Commander Keen and the original Duke Nukem.
 
Duke didn't have his red shirt yet due to these limitations. Or his sunglasses for that matter.

Now with VGA, you could have a palette of 256 colours of your choice. Here's DooM and Duke Nukem 3D's palettes as examples.
 
Games would officially ditch the previously more limited palettes around the mid-90s. And now we have higher colour palettes for PC.
 
Jazz Jackrabbit did have some oddities due to having different pallettes for things like art, levels, menus, and cutscenes.
The turtle enemies officially have purple shells. But due to limitations, purple was replaced with different colours in certain levels. 

Wikipedia also has a page about palettes based on different computer hardware systems.