Normally, troop transports do not approach the planet until either:
1) All weapon platforms are gone.
2) There are no more attack ships with weapons.
Were there no surviving attack ships in the fleet with the transport when it rushed towards the planet?
400 troops should be enough troops for any sized planet in stock SE4 (especially against the AI), assuming that they have shields, except possibly a filled ringworld or sphereworld. But how often do you see those?
You should probably not lose any troops if they have shields, and probably not very many if they don't have shields.