Anecdata, they might have had a system error. My Microsoft account that I use the free tier OneDrive on had the same email sent (you're over x% full, consider upgrading!). I suspected everything you did - eventually I logged in after verifying the email - nope, 5% usage or so.
I then went and deleted more stuff, but my money would be on a reporting glitch than a malicious money campaign.
I then went and deleted more stuff, but my money would be on a reporting glitch than a malicious money campaign.