When you fill the queu with the same type of productivity, it automaticly researches every level of said research

Did you finish your research normally or using some mod like Combat Research?

I have parallel research (more or less the name) that allows research different technologies at the same time

Yes, it seems to be a problem with Parallel Research, which I cannot fix from my side. Parallel Research sets researched = true to finish the research; this does not actually work properly for non-infinite multi-stage techs. They need to set it as a current technology then do progress = 1 instead.