This is part of the ongoing saga of trying to get Emacs to DTRT with
buffers popped up only to serve as info while Emacs asks a question
requiring a response.
IF you use a standalone minibuffer frame, AND the popped up buffer is
special-display (e.g. because of `special-display-regexps'), AND you are
on MS Windows (which automatically shifts the focus to a new frame that
it creates), THEN:
1. When you try to exit Emacs with active processes, Emacs pops up a new
frame for buffer `*Process List*' and asks you about killing them.
2. But the minibuffer frame no longer has the focus! So when you type
your answer (e.g. "yes") Emacs tries to insert it as text in buffer
`*Process List*'. Poor Emacs.