So I'm playing as PA (favorite faction), "The Art of War" GC (the one with 91 plantes) on Captain difficulty (because it's been a while lol). Every time that I try to conquer Ession after it's been taken by Rebel Scu-*ahem* the New Republic, when I play through the battle manually, any troops garrisoned on the planet will not show up in the battle, and the planet remains under the control of Rebel Scu-*ahem* the New Republic. But... if I autoresolve the battle (with crossed fingers, properly aligned stars, and a lucky horseshoe hung from the upper-left hand corner of the monitor no more than 3.125 degrees past vertical)1 and win, I will end up conquering the planet. And sometimes, that won't even work.
Now it just occurred to me that (having nVidia Shadowplay on this swanky new laptop and all) I could have recorded a video of the issue, but alas, too late. I will try to do it the next time I run into the issue.
Thanks!
1 Yes, I was being sarcastic.