Defensive armies can get some massive boosts, depending what's on planet. There's even a tech that just directly boosts them as well.I just played this version for the first time, went into a war where i out gunned the defending force by 5 times, broke thier moral by 10 times them, was a hundred troops stronger then them, the planet beat this army hands down plus the extra 500 points of men i fed into it, how is anyone supposed to play a game where the stats are bogus, somehow in this war that i controlled most of his territory decimated his fleets totally and everytime get a fleet of 6000 from nowhere from. i dont get this ability. i cannot generate the needed credit from systems to do that espeically if ihave taken out the strongest bases how can they. this was supposed to be a great strategy game but if from everything i can see that i am going to hands down win a battle and desperately lose it how is this so??? I really really desire an answer to this after spending so much money for a game that does not remotely live up to this.
Just because you have more troops (especially if there's a low combat width) doesn't mean an automatic win. If the defenders are "very strong" and have a good general for example, they can be a lot stronger than just raw numbers of troops would suggest.
Defeated ships aren't always destroyed. Sometimes they do an emergency withdrawal and come back once repaired. Alternatively, they may have had a fleet some distance away that took time to arrive. It's also possible that they're an ally joining in late, or that it's a fleet from the marauders, who are pretty much universally hostile.
I'm hoping you mean the fleet had a strength of 6000, not that it had 6000 ships in it. That would be distinctly unlikely.
Do you have a save you can upload from during the war? Preferably during the invasion.
If we can look at that, we might be able to give you a better suggestion as to what is happening.