Well, I'll be.  I'm seeing the same phenomenon in 3.5.0beta[3] in the PitchFactor.  I don't have the TimeFactor, but I have many Novation keyboard controllers.  I've seen spurious MIDI messages when the Novations get older and accumulate dust & debris.  That isn't the cause here.

But I ran the (no MIDI input  – THRU – Clock In) PitchFactor straight out from my MIDI router to Bome's SendSX MIDI monitor.  One quick test, and I'm seeing the same kinds of MIDI messages that you are, when turning the encoder.  I even got a few isolated Note Off messages, and some undefined F9&h messages.

For some reason, the non-System Real time messages seem to favor MIDI channel 1, or channel 9.  Very strange.  I'm going to experiment with this a little more.  Nice catch.