Exact same thing happened today in the system I've been operating in. We were on from 36% vs. 44.8% yesterday, but today my faction shot up to 44.3% while the controlling faction dropped to 27.5%.
Notably, the controlling faction
was in expansion from the system in question and, as it turns out, finished today and expanded into a new system. Unfortunately I hammered out like, 25 missions yesterday according to my inara logs, since I was pushing hard to try and make sure the conflict actually happened.
It looks like the controlling faction had the expansion tax taken off it which was enough to leapfrog,
then the missions went through and pushed the gap even wider.
@Dommarraa - were either of your factions in expansion in the days leading up to your leapfrogging? I know I've triggered conflicts in other systems since the carrier update and they correctly locked influence.