What happens if you leave hair dye on too long?

I don’t mean for hours and hours. The box recommends 20 minutes. However, it’s hard to judge. It probably takes that long to do all my roots. So should I wait 20 minutes after I am totally done with them all? Will the ones I did first be a different color from the ones I did last? It seems like if I leave it on too long the color is darker.