It sounds like you may have hit a bug that tripped up the script, perhaps. See if you can recreate it and do a report.
I'll do a few tests, or maybe just start a new playthrough and take notes this time to make sure my memory is not playing tricks on me.
Still, if using the tadpole with companions does not count maybe the warning shouldn't trigger... unless they will indeed count sometime in the future (it would make sense imho).
