Upon killing Chimera once the other day, and Hydra today, they just disappeared for me and then left the entire group of us in the instance. With no way to leave.

Each fight involved a lot of dead people, and use of the LB3 for the WHM. I'm not sure if it's the cause, but it's the only familiar link between the two fights.

The image below shows us stuck inside and no Hydra in sight.