Conditions cannot see units on transports, but triggers can affect them.
Example: a condition looks to make sure you still have a particular unit. If you don't, a trigger fires. As long as you have that unit anywhere on the map, you're good. But if it dies, the trigger activates.
However, if you move the unit onto a transport and leave it there, it is effectively invisible, doesn't meet the condition, and the trigger activates.
While playing around with this, I've further discovered that this is just conditions. Units on transports can still be affected by triggers.
Example: A trigger removes all of Unit B from the entire map, if the condition is met that there is no Unit A anywhere on the map. Say you have a Unit B on a land territory, and one sitting on a transport. If you have Unit A on land, nothing happens. But if you put Unit A on a transport and leave him there, then he becomes invisible, the condition is met, and the Unit B is removed from both land and transport.
This should be changed so that conditions can take into account units on transports.
Original forum post: http://tripleadev.1671093.n2.nabble.com/Units-on-transports-are-hidden-from-conditions-td7588107.html
Another forum post: http://tripleadev.1671093.n2.nabble.com/directPresenceTerritories-trigger-including-all-the-map-sea-zones-td7591146.html#a7591183