Here are couple rules
Ships at Port:
When moving to a friendly sea zone, ships can choose to enter a friendly territory.  While not at sea, the ships are not subject to combat nor do they interfere or add with any other ship movement, combat, or amphibious assaults.  Movement into the territory is free, but costs 1 MP to leave.  If the territory is captured while ships there, then they are lost (scuttled).  Land units may move to a territory and finish their move on a transport that is also in port.  At that point the transport can sail loaded to the adjacent sea zone.  Once a transport is in the sea zone it can unload as normal.  Ships must leave by the sea zone in which they entered the territory.
Mines vs. Transports: Mine hits on transports can be absorb by loss of a load.