I ran into this accidentally in Clone Campaigns, don't know if it's the same as in the regular game, but probably is.
I was playing Clone Campaign #2, mission #5.
Through the whole mission there's areas where neutral transport ships will drop in reinforcement troops for you.
By neutral, I mean they are ally ships but you can't control them.
Anyhow, not being able to control these transports, you can STILL load your troops onto them like normal (the troops will move to the transport).
But once loaded, you've basically lost those troops for good because you don't have any control over the transport (can't move it, can't unload, can't Del it, etc).
The dev team should have disabled the Loading ability of transports (when you have units selected and right-click the transport), because by accident some players could send units to the transport without realizing it's an uncontrolable neutral ship).
2 cents.
I see your point. But if transports can't load what's the point of having them?:confused:
Good point. A good thing to address in a patch. Besides to stop the Shrinking Padawans!
"But if transports can't load what's the point of having them?"
In this case, the developers are using those neutral uncontrollable transports as part of the plot for singleplayer.
The player actually see's re-inforcements dropped off by transport, which is more tangible than units popping out of thin-air.
Do you play much singleplayer? hehe...
Maybe in a future X-Pack...