Yes it seem like if you are attacked and you have extra (more ship in numbers) then at least the extra transports should be able to retreat, rather than having to stay there and say that the one remaining (sub for instance)can take out the million transports that are left.

When a plane does a flyby and there is a ship and a transport and roles a hit does it take out both?

when doing a amphibious assalt with a tank can it blitz though a freindly or unoccupied teritory

Yes we are also having that problem I was wondering why a transport could not retreat while your other ships were fighting?