Expanded Galaxy Mod question

I could not find anything on the subject of the mod's war assets changes. I'm doing a shittiest-outcome type run and my war assets have only gone up throughout the game despite assurances they would lower as missions progress. I currently have 4400 total MS right before assaulting Cronos Station and this is far too much for the worst ending. Haven't done any side missions or scanning at all. What gives? How can I fix it?