Well, I haven't been able to reproduce the mixed mark reinforcements so far, but it is pretty trivial to show mixed mark guards at game seed. I'll see if I can "cook one up".
As for the Mk. V ships on the Mk. IV worlds, there is actually a pretty good mechanic to explain that, Mk. upgrade "trade-ins", where the AI can scrap 2 ships of a ship type Mk. N to get 1 ship of that ship type Mk. N+1. Among other things, it helps keep the number of ships in the game pruned a little bit.