No sweat. Confusion is pretty much a given when the procedural posture is complex, and "stay" is used as an action against Trump's EO, and as an action against a court.
This is a messy decision. SCOTUS is trying to save face and cut the baby in half. Unwise, but hey, it's SCOTUS, known for being unwise.
It seems the “relationship” part of the order is pretty vague....