That first cypher detonated because a new cypher was activated by Snake. Since there can only be one cypher on screen per Snake, if you use a cypher, let go, land, and activate a new Cypher before the old one leaves the play-field, the first one blows up in a minor explosion. And the only way to activate a new cypher as far as we know, is to take damage after you have left the cypher, and as is clear in that video, that Marth was nowhere near Snake when he got off that first cypher. Marth did not give Snake that new cypher. Either this is a glitch in the game, or... a loophole... thing... that allows...
Yeah, it's a glitch.
We must study this video to find out how this happened. Then recreate it. FOR SCIENCE!