Afaik evolution factor only gets increased on a) time passing, b) extra pollution, c) destroying spawners - https://wiki.factorio.com/Enemies#Methods_of_increasing
This mod does neither of these things by default, but if you've enabled "wisps fight biters" option, they totally can start killing spawners and hence increasing that factor.
If you have that disabled already, dunno what else it might be (except fallback "factorio bug" option), maybe you know what does it?
EDIT: oh, also, can suggest checking other mods that might do any of 3 things above (e.g. creating/removing pollution in spikes or something).