Multiple emails can be sent out for single logical action

It's possible for one logical action to happen partially before an activity collection and partially after the collection, causing more than 1 email to be sent. For example, I ran into a scenario where a number of files were uploaded at the same time and I received 2 different emails for this.

We should find a way in which this can be avoided. Ideas include not collecting when an activity has taken place in the last minute or automatically scheduling an activity to be collected during the collection after the next one.

Doing something here might also make the email aggregation more effective.
Is there a risk that activities taking place during phase 2 and phase 3 will end up being lost?