Yes. It can be confusing locating the source of the beep when there are several sources of /beep, including scripts, options\sounds\events, highlight, the 4 kind of options\sounds\beep-on-message, etc.
Something like this, or an identifier like $lastbeep or an icon in toolbar that gives a tooltip showing the cause of the latest beep.
Or even something like a /scroll_all_windows_to_bottom command
The most common cause is as mentioned by OP, often caused by the mouse accidentally scrolling up slightly without realizing it.