Each of the 21 Havens possesses Spawn Containment and Research Super Facilities which are honeycombed throughout the sub structure of the Haven.
Before the Annunaki went into hiding, they used the Havens as Spawn 'Research and Containment' Platforms, to help them hopefully find a weakness to The Spawn. But when the Spawn evolved into Daemons they had to abandon them and the specimens still inside and flee.
The first facility discovered by Humans was discovered on one of the 3 Havens located in the local Superuniverse. The Metatron supposedly engaged a tractor beam, having de facto control over the entire disc, causing The Gnashbone Fury to crash right on the entrance to the facilities, thus causing the MSWG to have to go investigate, and thus, find the facility, thus free The Spawn, thus, engage his plan.
The second facility was discovered on The Mantle, as the same purpose as the ones on the other Havens, only the freeing of The Spawn in this particular facility was caused by Zodiac Fiends.