It has to do with planetary invasion mechanics. Check out the WIKI, http://galciv3.gamepedia.com/Ground_invasions . It was very enlightening. It explains resistance and the most important factor, planetary defenses. If Planetary defenses are at 75% (from an Elurium Shield for example), then you lose 75% of your troops before they even land. You can get planetary defenses well above 100% as well, without the Elurium Shield, using high end techs, or smartly placing the military buildings for max Adjacency Bonuses (and if you have a Military Bonus tile, its even easier).
Planetary bombardment can help nuetralize planetary defenses, but a) its expensive
huge pop death on enemy side, who you want to keep, or atleast have them replace YOUR losses c) huge approval hit. I havent tried BIO or Informational warefare. Info Warefare would probably have no approval hit, but probably not as affective. And those propganda fliers and the fuel to drop them can get expensive as well 
In your specific case however, they must have had good defenses (resistance and planetary defenses). The proof of that, is that the surviving pop was less then your losses, so yo took a net pop loss, which is never good.