Yes. Because you know the composition of positive controls, you can use them to calibrate other parts of the process. Just like you said, if these three mystery OTUs appears in your second batch of samples, including your monoculture control sample you ran on both Illumina runs, you could argue it's artificial and remove it.
It's possible that the second batch really does have a highly abundant g__Proteus in it.
Here's some more discussions of positive controls and filtering out strange microbes, if you are interested:
