Surgery on infant plants is not dissimilar to surgery on infant kids. Everything is so small, it's easy to screw it up.
Instead of 'topping' them, you've given 'em a 'FIM'. (Fu*k, I Missed)
If you 'pop' the tops off instead of using scissors, this event isn't as likely to happen. Being such a young plant though, damaged cells rebuild and sometimes the youngster get's the reapirs wrong.

After butchering them this early, hopefully the stress won't stunt them and prevent a full recovery. They aren't healthy (mature) enough to dick with yet, but you knew this already. Usually happens if you don't slice between the youngsters nodes, and leave some part of the mainstem.

Looks like overwatering and a lack of perlite, too. What kind of soil?