yes there was a bug with disable during action indeed, it was fixed in 7.17
Sounds like a bug, I suggest checking the patch notes, and see if this is fixed in one of the following versions.
As a workaround you could place an intermediary pop-up page with your confirmation, and then add your microflow on the "Yes" button without the confirmation (I think this should work as expected).
Hope this helps
you could have 2 buttons that are styled the same.
have them in conditional visability, and in the micro flow switch the 2 out.
This is a pretty dirty way to fix it, and like Dragos said, its probably a bug. but it might solve the issue if you need a quick and dirty fix