Great game! One sort of odd thing I noticed around level 15 or so, really just because the levels were getting longer, is that blue and yellow were really common around the beginning of any given level, then red would start to mix in, and the second half would only have red mana. I was playing with a full set of four, and every mana color was represented, so I'm not sure why that is.
I think it's true Random; which contrary to what one might imagine means you might see paterns, as anything is possible. Maybe the author does drop by and correct me if I am wrong.
You can easily control it by having jasper with the "When you get one mana, you get 3" common ability, and it never becomes an issue, or by having only 2 heroes for simpler mana distribution.