I did a search and did not find this specific occurrence reported. Here is what i found.
One of my bases was being attacked, I selected to enter the mission, did not change any settings on the next dialog box, equipped the soldiers in the equipment gui, then entered the mission. The base mission map appears and then immediately goes back to geo-scape leaving that base in red alert status. I tried to enter the mission multiple times. I also tried with the kill live aliens selection checked and un-checked. I then noticed that there were multiple new messages in the message log, "You cannot process aliens yet. Alien containment not ready in this base.", one for each attempt.
The base in question does not have an alien containment. This has not affected regular missions, other than not receiving the alien bodies upon completion. I would speculate that the selection during a base attack that gives the option to kill all aliens in containment does not take into account that there may not be an alien containment on the base. Just a guess as i have not looked into the code.
Doing an auto mission allowed me to win the mission, so it is possible to work around.
I am playing the 2.3 release version on normal mode. Hopefully i am not repeating something already submitted.