I cannot reproduce this, but on occation, the Planetary teleporter, Warp Rails, and harvester floor upgrade effects appear without the research.

Yeah, we saw this too. Not sure what causes it and I don't really feel like deep diving it since there's no gameplay impact, but if you or anyone else figures it out, would be happy to code or merge in a fix

I figured out why this happens while trying to update to IR 3.1. IR adds a new force for the Manifesto simulations and researches all techs for this force. Warptorio does some weird abstraction causing it to not handle resets or multiple forces properly.

I don't know if it's possible to fix without forking Warptorio because the remote interfaces are not documented. Anyways, consider it a gift to make this mod a bit easier :)