I think the problem is here: as Radiant Phoenix said, maybe you should wait for the transport to finish unloading. I suspect that, as a gate is very fragile, you killed it with the 10 first ships unloaded by the transport, then ordered these first ships to go back in the transport... I think the logic for the transport unloading is this: when you give it the order to unload, it unload 10 ships, wait one second, check if it's empty, and if not empty it unload 10 more ships and repeat the loop. So if you "feed" it with ships before it's empty, it will continue to ask itself "Am I empty? No? I continue unloading." Until it's empty, stops the loop and stop unloading ships you load into it.
Maybe it's that, or it's a bug, but transports can definitely be reloaded. They are intended to, at least.
EDIT:
I just saw your post before posting mine. Maybe you can post a Mantis suggestion to make transports stop unloading when they are loaded while unloading. Sounds like a good idea.