I thought this thread has agreed that Cloud was in SOLDIER, for a while, but wasn't successful enough to stay and advance. Low ranking SOLDIER members also wear the outfit of the standard Shinra footsoldier, as seen by the SOLDIER member studying in Junon during your first visit, and seen many times during Crisis Core.

So both Cloud and Johnny could have been in SOLDIER. But as to what happened between them... No clue. I doubt it is the destruction of Nibelheim, because Johnny wasn't there and had no reason to suspect Cloud of being there. Unless Johnny was the unnamed soldier who fell off the bridge during the Nibelheim mission and couldn't be found afterward. In which case Johnny's phenomenal luck shows up again with his surviving Sephiroth's rampage...