Title is self explanatory. This happens with both the normal sound variant and the "wait until" variant. I haven't tested to see if the "wait until" variant will cause it to continue to read the script afterwards yet. In general Snap seems pretty bad at stopping all the scripts when the green flag is pressed, but this was something that stood out to me. (If it helps at all, I'm using Windows 10, with what I think is at least one of the latest versions of Firefox)
This is one of the differences between Snap! and Scratch
The philosphy in Snap! is that the pressing the Green flag just launches all the scripts with a Green flag hat - it doesn't do anything else.
Here are a few threads on the subject
https://forum.snap.berkeley.edu/search?q=green%20flag%20stop
i also experience this as well. clicking the stop sign stops the song
Try this:
[scratchblocks]
when gf clicked
stop all sounds
. . .
[/scratchblocks]
Oh. I don't know how much I like that, to be honest... I don't see how having the green flag button not restart the project is useful for anything other than tripping up new users /:
Scratch's aim is to make things as simple and easy as possible
Snap! has a higher aim and decided that Green would just be for Go , Red would just be for Stop - a cleaner concept with no overlapping ambiguity 
I guess it's less ambiguous, but it sounds like it would lead to a whole lot of extra debugging for larger projects. I ran into problems with it even when working on my tiny projects.
Once you get into habit of pressing stop before Green flag - the previous Scratch method fades from memory.
It caught me out as well, when I first started using it for real projects, but now I don't even notice
I'll take your word for it... If your prophecy is untrue, I will be back... for revenge! 
We aren't purists about the green flag semantics. For example, it deletes temporary clones (as does the stop sign), so people don't get exponential growth in numbers of clones. When you load a project, generic WHEN blocks don't work until you click the green flag (or otherwise start a non-generic-when script).
But anyway, intuitively, the green flag is about starting things, not stopping things. You could imagine a music program that wants to play two songs simultaneously, and each green-flag click starts another one.
I feel that the clone deletion makes it even more confusing /: As for the "intuition" thing, my intuition tells me that pressing the green flag will do the same thing as loading the page for the first time: Start the project from the beginning. I see what you mean by it not being a "restart" button, though.