I'm about the clumsiest person I know, and I've pedaled standing with my left foot (the one I put down) on the underside of the pedal because I (clumsily) missed the engagement of the pedal and didn't have time to flip the pedal around to clip in. I wouldn't recommend it, but learning clipless is simply a matter of time and experience, and no matter what system you use, this will always be the case.
I remember riding with a guy who was a guest on a club ride who would disengage both feet, then put them down as he came to a stop. I told him that he was asking for his cash and prizes to be mashed to a pulp, and told him that he needs to only decleat one foot (have to decide which one he preferred), and that way he won't crush his junk on the top tube when one or both of his feet get caught on the ground with the bike still in motion.