Sounds familiar to me (we are working with Windchill 10.1 M040 and Creo Elements/PRO). Users forget to check if the action took place, and both environments (WC and ProE) are rather poor in warning the user when an action didn't took place.
For user 1, the checkin didn't took place (for whatever reason). For user 2, the save didn't took place (for whatever reason). Reasons can be divers: access rights, regeneration status, family table conflicts, etc.