[Master Belisarius]

AJC:
"but this time the transport disbanded from the fleet and attacked the planet on its own and was wiped out by planetary defenses...."

This behaviour is right: first the ships with attack capabilities, try to defeat the planet’s defences, and if they have success, the transport with the troops try to take over the planet.

Atraikius: I did my tests using standard ships as transport troops. Really I don't know if the AI have problems using Transports instead standard ships.