I'm having an issue with my Endless Moons mod.
Minor pop bonuses that looks for an anomaly aren't working.

Endless Moons makes a slight change with what counts as an anomaly, namely the moons no longer count. To accomplish this, PlanetAnomaly no longer adds to OwnedAnomalies, and instead the individual anomalies add it themselves.

For every other use, this works and counts correctly (it works for system improvements, laws, and minor assimilation affinitys) But for some reason it doesn't work with population bonuses such as Pilgrims' ClassPopulationPlanetModifiersTraitSecondaryScienceAnomaly01 (This particular item adds BonusPopulationScience of 3 * PlanetHasAnomaly)

I've looked at the in-game values using the modding tools, and all the relevant values of AnomalyCount, OwnedAnomalies, PlanetHasAnomaly are correct. (In the above case, PlanetHasAnomaly is indeeed 1, both on the planet and population properties)

I constructed a test where the pop bonus trait instead just adds a flat value so as not to rely on anomalies. It still would not show up.

This seems to mean it's not the anomaly counting math.

I have no idea the problem, and I'm starting to think there's an undocumented DatabasePlugin that needs to be loaded because I made changes to PlanetAnomaly.

Any ideas?

I compared what you had to what the game loads, it doesn't appear as if there is anything else relating to anomalies that you are misisng (there's some random ones under EntityActions but you probably already know that).

The only thing I could immediately see could cause problems is that you might've removed the following line from SimulationDescriptors[Planet] line 172

<Modifier TargetProperty="PlanetHasAnomaly"            Operation="Addition"    Value="$(PlanetHasAnomaly)" Path="ClassPlanet/ClassPopulationPlanet" TooltipHidden="true"/>

Reason I think this is is because System Improvements, Laws, and Assimilation Traits all use the ClassPlanet value (or at the very least, should), whereas the Population Modifier Trait version uses the ClassPopulationPlanet value. This is the only thing I could find relating to PlanetHasAnomaly that could cut the connection between the ClassPlanet and ClassPopulationPlanet version, so if that's not missing it's probably something a lot more complicated.