Well, considering at the same time (SPOILER)President Shinra was killed by something (dunno if that was a clone, or Jenova running around) then something was there to open the cell for Cloud. I'm going to go on a limb and assume that it was (SPOILER) Jenova, since it had broke out of its container. It wanted Cloud to be a part of the reunion so it had him released. Don't take that as a fact though... I'm merely speculating.