Do you use the "Restore Previous Session" feature of your web browser between reboots? Do you use keyboard controls to open new windows like Ctrl+N?

If yes to both, chances are that your mystery window had remained part of that continued session, and was reactivated with a Ctrl+Shift+N or equivalent. Shift is right next to Ctrl so if you fat-fingered a Shift at the same time that could explain the apparent necromancy.

As to where it went originally, you could have moved it to a different virtual desktop, moved it off-screen accidentally or, heck, even misclicked or miskeyed to have it actually close. A reboot would then have closed it for certain, except for the fact that it was still lurking in your session.

Another thing that can cause windows to move around is when a HDMI or DisplayPort monitor disconnects. Unlike with older connection types, those disconnecting is detectable and modern window managers try to "save" windows by throwing them on any remaining active monitors. If you have both types of monitor connection, or had at some point in the past, it could be that your mysterious window was lurking on a screen you couldn't see but the system still thought exists, at least until it was closed for certain.

Admittedly unlikely, but you could rule that out by checking the system monitor arrangements in the settings.