1) Alien corpses can be stored in a base without containment, but only so long as the game isn't reloaded. After saving/loading, they are gone. So, depending on the expected behavior, either they should need to be transferred to a base with containment (or deleted if there's nowhere a containment), or they should not be deleted during a save/load cycle.
2) If the alien containment is destructed early on, researching hovernet and blood spider later on is impossible, as only their combat versions still appear, together with all technologies depending on those.