Nope, it does. Has since the beginning. On three separate widely spaced (measured in years) attempts, Apple Music replaced tracks in my library with other tracks. First time was the original trial, the second time was well after the trial ended, and of course they must have fixed the egregious bugs by then. Not. The third time was last year.
Ref:
https://discussions.apple.com/thread/7142385 for examples from people experiencing the same thing.
It boggles the mind, how there could actually be a design goal that would replace local files under *any* circumstances. It's more or less a bug in the process that allows machine A to upload a file without supervision. Apple Music then matches a different file, combined with another bug in the process that machine A should be able to download files it does not already have. Well, that's right, it doesn't have that file, because it was mis-matched.
But it does it anyway. Been there, done that, ran the diff against the library backup.
And I'm not the slightest bit interested in it uploading files from the local library in any case. Whyinhell would I be? Whyinhell would *anyone* be? Why can't that be turned off? But Apple conditions a significant portion of Apple Music functionality on you allowing that to take place.
I used to think Apple paid smaller license fees if they could show that you owned the track they were streaming to you. But since they replace one track with another, that can't be the control.
And years later, I'm still wondering how they're getting around the fact that the user almost certainly does *not* have a distribution right on the file(s) that're being uploaded, since that user is almost certainly not the copyright owner. Apple must have one *hell* of a contract with the major labels.
There is always so much to it, really. With millions of available songs, etc., there are hundreds of millions of combinations and possible outcomes. Various albums - live, remasters, etc. There is also the impact of artists dictating what versions can be available via Apple Music. This is only a small, but still impacting element.
I can give one real world example, as simple and straightforward as it can get. I do absolutely see mismatched songs to the degree of it being the same song, per se, but a different version.
I have a Def Leppard album - Hysteria. LP version, imported straight from CD, 2011 is when the file notes it was imported. It shows as the original file (Pour Some Sugar on Me) in the library on my primary iMac - the one I've maintained for years - farther back than 2011. This iMac, for reference, is a Late 2013, presently running Mojave with the Music app, not iTunes. So, it's been through many upgrades, migrations, etc., since (before) 2011. Additionally, I have always imported above 256bit, which takes the Match upgrade out of the equation.
Now, I can confirm that this song is still the original MP3 file on that iMac, in the Music (iTunes) library. However, on no other device, iPhone, iPad, iMac(other), MacBookPro - in either the Music app OR iTunes, can I ever get that version to play. It is always at least the remastered (different intro) or live version. Annoying, to say the least, but one thing I can undoubtedly confirm is that the files on the original Mac, in the original library, have not been replaced by either Match (which I had for a few years prior to AM) or Apple Music since - and I use this song only as a specific example, but this exact behavior occurs the same with many, many songs, as I copy a vast amount (~32GB) of my music directly from my iMac library to a USB for my truck, to have a local copy of the right music instead of these matched files from my iPhone - that is more secondary.
Now, I know that my case is not the same as everyone's because my library is not the same as anyone's - you'll never find any two person's libraries alike. Ever. But we're talking about computers. They don't pick and choose what data goes where, they do YES/NO computations. I will always feel that this is more likely user originated, from thinking that your music actually exists on your iPhone/iPad/iPod from sync and can be imported to a new computer, to thinking that once your music is matched, your local library can be deleted to save space. Or, the more common of events, computers get replaced or reinstalled with no actual file backup. These are very simple, common mistakes that lead to you getting the incorrect music while using either Match or Apple Music with iCloud library sync. But when something doesn't do what it's expect it to do, even if the expectations is incorrect, it's always someone else's problem first.
Again, and final thought - I believe this can and does happen in some scenarios. I can't prove or disprove otherwise, given the variables. I am just trying to say that it doesn't always, and more likely than not, doesn't happen as often as claimed.