If methane could do it,why not carbon dioxide? Or any other trapped gas, such as what might come from a submarine volcano?

As for seeing such a thing, perhaps it has happened and was thought to be something else, such as MMario suggests above. The seas are full of strange reports.

Flicking a lit cigar butt overboard at just the right moment could have interesting results.

Are whales subject to flatulence? If so, could some of the whaling ships that have gone missing have been the victims of a pod of conniving, flatulent, whales?

Seems to me that the chances of a ship (small object) being at the edge of a methane bubble (random happening) in the ocean (huge object) at the right time would be vanishingly small. Not impossible, but approaching zero.