I have the same problem - during many battles, I get thrown out of the battlescape, and it's like the battle never happened. This crash always happens during the AI's turn, never during my own. Here is the log of my latest reproduction of this bug:
updateact2012/12/01 23:21:37 (player 0) It's team 1's turn!
2012/12/01 23:21:37 Quizer has taken control over team 1.
2012/12/01 23:21:46 Soldier entered the rescue zone
2012/12/01 23:21:48 Soldier entered the rescue zone
2012/12/01 23:21:53 Soldier entered the rescue zone
2012/12/01 23:21:55 Soldier entered the rescue zone
2012/12/01 23:21:56 Soldier entered the rescue zone
2012/12/01 23:22:01 Team 1 ended round
2012/12/01 23:22:01 Team 7's round started!
2012/12/01 23:22:02 [STATS] alien (Akrokk Tt Treknk) kills civilian (b c) with Snap Shot of plaspistol_ammo (entnum: 130)
2012/12/01 23:22:05 [STATS] alien (Uoorgh Zr Zus Soufz) kills civilian (b c) with Snap Shot of plasrifle_ammo (entnum: 128)
2012/12/01 23:22:07 R_AnimChange: No model given (walk)
2012/12/01 23:22:07 LET_StartPathMove: Could not change anim of le: 138, team: 7, pnum: 9
2012/12/01 23:22:07 ********************
2012/12/01 23:22:07 ERROR: LE_DoEndPathMove: Actor movement is out of sync: 157:128:0 should be 159:137:0 (step 2 of 2) (team 7)
2012/12/01 23:22:07 ********************
2012/12/01 23:22:07 Shutdown server: Server crashed.
2012/12/01 23:22:07 Unload the game library
It seems the problem has to do with alien movement - apparently the alien isn't where the game expects it to be. It always happens to aliens, not civilians (all my occurrences of this bug say 'team 7' in the error line). It seems to me that this often happens when the aliens are shooting around a lot, but since only deaths are logged and violence may happen off-screen (as during this particular trial run), it is impossible for me to confirm either way.
If I retry the mission enough times, I can usually get to the end without this happening within a couple of attempts, but it severely hampers my enjoyment of the game. I decided to get the stable release instead of a development version, but this isn't turning out to be particularly stable.
I'm pretty sure this problem has long since been fixed, and I would like to know if a patch exists, or, failing that, a workaround, or whether I'll have to get a more recent development version to avoid this problem. I tried looking over the bug list on the sourceforge page, but wasn't able to find this bug among the huge number listed there. I also wasn't sure what version the 'open' and 'closed' tags apply to - just because something is labeled as 'closed' and thus presumably fixed, doesn't mean this is the case for this release which is more than half a year old now.
Anyway, if someone reads this, please let us know if there is a patch or workaround for this bug.
thank you for your time
Quizer