I have noticed now on multiple runs on Necrotic Wake, Spires, Plaguefall so far that the % does not add up.

According to the addon i was supposed to have 103,5% i even took some extra just in case. We killed the last add on Necrotic Wake before the third boss and we were on 98%. Similiar things happened on every run.

If you are able to share the DungeonTools route, and ideally a warcraftlogs link to one of the runs where you experienced this, I could try looking into this.