I had 2 Arthrons and a Scylla in containment. I mistakenly removed/destroyed an Arthron instead of harvesting it, so I reloaded and presto chango containment is now empty!
Danforth Update - v 1.0.58746 - 11/06/2020
Fixed an issue where the player’s containment was emptied after loading a Geoscape save.
Pandorans captured go to containment facility as expected, and do show in there. However, after that if you load a save then they all disappear and containment shows a zero count.
Have submitted a bug report in-game via the reporting tool as well.
It appears that this happens anytime one loads a save while in game. A load after just starting the game does not empty containment.
@Michael Carver: Be good to see a post from someone on having put Pandorans in containment, saved, reloaded and then what happened.