I've had this more than a couple of time now. Ships in port defence aren't landing or having trouble in landing. I can sometimes get one of them to land as normal. They just stay there in the water after giving them an order to land. You can still give them an order to move anywhere else except to land. Though the last time it happened I did get them to land some way off from the settlement they were defensding.
Haven't noticed this happening to the ai when they are defending.