Let's talk about Hunts - a detailed rundown of their assumed mechanics

[Vandesaan]

Our most recent mindflayer popped at 5:45pm eorzea time. I know he popped right ontop someone in my hunt LS that was doing Spiritbonding in Urth's.

He died 6/13/2015 1:56:00 am pacific time. <- can you check if this calculates to night 2 or 3?

Maybe we just didn't manage to pop him the previous night or something.... and that was the third night? (Since you mentioned mindflayer and croak are landmined.) <- this would probably also be why my understanding of when the S's pop is messed up because no one's hitting the landmines in a timely manner to pop them XD

That would be on the second night, but it's supposed to start being able to appear around midnight on the second night. Your kill was at 7PM on the 2nd, which is strange. We know for 100% certain that he can not spawn during the day, so I can only assume nobody stepped on the landmine

edit: to clarify, I mean midnight as in 00:00 on the 2nd night, 19 eorzean hours before you killed it.