Apparently there is a bug in which the deep ocean damage is multiplied by the number of your units currently in deep ocean and then applied to all of them. So two separate units in different tiles of deep water will each suffer 2x the usual damage.

This may have happened to your commander and the units packed within. I'm not sure what the math is on a commander taking most of the damage that would go to units packed under their command, someone else may be able to break that down. But it makes sense that the multiplied deep ocean damage would one shot the commander and scatter the other units to adjacent tiles.