This situation happens if you have a recurring event, e.g. every Wednesday at 4pm:
Every time you save the parent event, the sub-events in that series of recurring events are saved as a new ID (i.e. they are recreated and their ID is changed).
The result of that, is that any bookings that were already made on those events become orphaned.
What needs to happen is either:
1) Saving an event in a series does not re-create the event and thus orphan the bookings
or more likely
2) The plugin automatically moves the bookings to the new ID
It really would be great if we can get a quick fix to such a fundamental thing, and we'd be happy to do testing of a beta of the plugin if that is fixed.