Marie Severin did most of the coloring, as I recall, and she seemed to do this whenever she felt the balloons needed to be made more distinct. You could tell when she was rushed, too. She'd make the figures in a panel all red or yellow or whatever.
I read somewhere that, when she was working at EC, Marie would color some panels dark blue to show she disapproved of the shenanigans going on in it. I've only read a handful of original ECs (not reprints) but I didn't notice this.