You can't click on a boat that's done moving so you can't unload any units even if they have movement points left. The solution is to activate the units while the boat has movement left (e.g. right before it's last move):
Click on the boat, then one of the "S" marked transported units in the unit stack window. Keep clicking the (now blinking) boat and make all units "W". Units that don't have movement left because you loaded them this turn, can't be clicked and will stay "S". Finally, click the boat in the unit stack window and move it.
PS: Don't choose "Wait" for any units. They will go back into unclickable state again when you move the boat.
If you find yourself with a nuke that can't make it back to your carrier or town, take it to one of the enemy's irrigated squares and choose PLUNDER. The nuke won't crash, but it will destroy your enemies irrigation system.