Back in the days when there were less maps we played every map back to back
Ooh a little higher, now a bit to the left, a little more, a little more, just a bit more. Oooh yes, that's the spot!
The rules clearly state that there should never be more than 2 cubes of a given color on a tile during set up, but they don't repeat this restriction in describing cube replacement during play. I think the limit clearly applies here as well: there are only 5 gray cards.
Also: I assume that replaced cubes are placed back into the draw bag (and not discarded).
Actually only the more recent rules actually mention the two cube limit, the original ones do not.
Realistically it is only relevant to the grey cubes (and possibly if you pulled four blue cubes for the four tile). We just play them how they come out. If we did pull three grey cubes we would replace one, but it hasn't happened yet in all the games I have played. If three or more yellow or red cubes come out then we just leave them be.
Yes they would be put back into the draw bag.