Is there any way to alter colors that are assigned to players? I am constantly being attacked by brown and green enemies, because I am having issues noticing these coloros on map.

You can only swap player colours if you use the map editor to modify the individual map and change which player owns which object. If it's a map with 7 or 8 players, you're sadly out of luck.

If you're using the HD mod, the Tweaks tab in the launcher has some values (that start with OpenGL.Colors) that you can experiment with and see if that helps with visibility.