Safari on MBPr late 2015 (OS X 10.11.6) makes a "Pop" sound randomly. How to stop this?
OK, the problem was one of the programs making a notification, while the display banner for that program is turned off in my notification settings, resulting in only this pop sound alert (without displaying anything). That caused confusion.

The solution was to disable these notifications whatsoever. If you have similar problem – check your notification settings and look for programs with banners turned off, but with the sound enabled.