Invisible troops in a 1.25/BM1.04 game

I landed 300 troops on an enemy colony and conquered it.
Next turn I moved the troops back to the transport and went to the next enemy colony. Transport ran away from the planet.
Checked transport, no troops found.
Looked at ship list with cargo setting and it said my transport had 300 troops. Transport still says it is empty.

I didn't have the chance to get back to my home system and pick up more troops before upgrading to 1.33 with BM 1.05. I was able to fill it up with population. I guess invisible troops don't take up any space.

In the same game, I landed 75 troops on an enemy planet with one small fighter and one militia. None of my troops will attack them. They don't need ammo, just supplies and were full up on supply. They just sat there spinning in circles getting shot up by the fighter. The enemy troop was injured but my guys wouldn't go after him. I tried to drop another load of troops but the game won't let them land. After they all got killed. I dumped 100 troops on it and the same thing happened. What a pisser.

I think the game can do without this ground combat system. With SE4 I could conquer several colonies in one turn with one transport/fleet. Now I'm lucky if the system lets me conquer one.