Yesterday I had one of those days.
Starting up Cubase, load a project from a few weeks ago.
Listening to the track, the lead vocal was a bit loud, so I turn the fader down and nothing happens. ?
I then realized that the track is running through an outboard compressor, adjusting that and nothing happens ?
I start to mute tracks from the first track to the last, everything mute’s except the vocals ?
I press the global mute button to unmute everything, and boom now the acoustic guitar is really loud as well ?
Checking routing, monitoring and sends, all as it should be ?
Then it hit me, hidden tracks, the acoustic guitar track had an earlier track that I had muted and hidden. By hitting the global mute button it got unmuted.
One down one to go, the vocals was still playing even if muted, even if I muted the part itself.
And then after chasing this for nearly 30 minutes I got the big Doooh moment.
I had Melodyne as an insert in a post fader slot. Melodyne uses its own audio recorded from the track, and being post fader it was plying no matter what was done on the track 
Haha!
Similar senior moment…
Was setting up to master m-s style on my outboard and couldn’t figure out why the return was only coming in with one channel. After 15 min, I shut the system down and went to bed. Figured out the mismatch in a few minutes the following day!
I’ve also had the same thing happened as what happened with you. Now when I abandon certain tracks, instead of just muting them I also pull the faders all the way down and shut the sends off.
I’m in the habit of even disabling them 
Have to admit to that one too once or twice…
Melda has a plug called MCompare, in a way like Magic A/B. Clicking can play a reference track, and unclicking plays the project as normally. I can’t tell you how many times I have been making changes to a track, increasingly wondering why there really isn’t much change to the sound, only to realize it’s the reference track (earlier version of the project) playing in the background on the minimized MCompare. Doh!
I’ve taken to turning off the power every time I minimize MCompare now. But yes, those “Invisible” Cubase tracks can play havoc too, I think I started a thread about that some months ago.
I’ve had a few similar “wtf is going on” moments like that.
I’m reminded of that old computer adage – Computers do what you tell them to do, not what you want them to do.