Thanks for all your reports and feedback, people. For sure there is something wrong with saving game process (or loading) - not everything is being parsed correctly, it seems. The strange thing is that for sure works two-three days before release, I heavily tested everything. Currently I am out of ideas what can cause this, but that kind of issue for sure has to be solved for 2.1.1 release (which is mainly designed for bugfixing, no new features).
Maybe you can experiment more in various ways. Try to not build/produce/research anything in bases, but go to missions, save, load, check whether bug still occurs. Then try to narrow things a bit. Try to unhire all personel, let several missions pass through and then save/load (maybe autoheal feature?). Try to finish the missions without being injured (/killteam 7 in the console kills alien team). And so on.
At this point any feedback would be helpful.