Sea transport stuck in Rome

So you can't make sea units in Rome but somehow my transport got inside and I couldn't get it out. Not that big of a deal just a minor annoyance.

Yeah it's not a port city, it should never have been able to get in, but there is probably a land bridge allowing you to.

But a transport/Destroyer close to rome, and try to merge the two stacks, thats the way you get the transport to rome, and so it can leave again

Yes you can get it back by putting another transport near it and merge the stacks. The transport probably got there either because you attacked an enemy unit with the transport, in which that unit's target was Rome or because you attacked a coastal city with the transport and a few units on the same movement as your opponent, so your transport followed your enemy's army to Rome.