To trigger this:
Enter Customize mode.
Create a Menu Button (MB).
Create a 2nd MB and place it inside the first MB.
Set some action for the 2nd MB to preform when it is left-clicked.
Right-click the 2nd MB and click "Hold or right-click to drop down".
Create a 3rd MB and place it inside the 2nd MB.
Exit Customize mode.
Open the menu for the 1st MB.
If you hover over the 2nd MB long enough to make it's hover menu appear and then click the 2nd menu button it does nothing.
If you click the 2nd MB before it's hover menu appears then it will preform it's action.
I'm not sure "Hold or right-click to drop down" is intended for use with menu-buttons. The bug may be that it allows you to combine those things in that way at all.
Even if you uncheck "Hold or right-click to drop down" and you click the MB's arrow to show it's menu, clicking the menu button still doesn't work (either way -- if the menu is displayed then clicking the Menu Button does nothing until you somehow get the menu to disappear).
It's your program to change how you like, but I'd rather it stay the way it is, than you guys remove the ability to hover over Menu Buttons to show the menu.
If you open the sub-menu, you have to close it first before you can click the button.
(That works best at the top-level. Putting menu-buttons inside sub-menus doesn't make a lot of sense to me.)