I am pleased (sorry don't take that the wrong way!) to see more affected users posting in the thread, and giving feedback to Apple.
To confirm my set up:
I have POP in my Outlook on my Windows 7 laptop as my "master", messages delete from server once downloaded to here.
My ISP is Westnet and offers POP and IMAP.
My HTC M8 phone is on IMAP set to 1 days messages so I can see what's happening during the day.
iPad Air 2 set to POP. Used to keep messages and attachments I wanted to have easily to hand. (Do not have Mail going to icloud).
SInce this IOS9 problem I have now changed my settings so mail is now left on the server, and have IMAP (😠) on my IPad.
Re getting the POP bug message out, how about creating a thread on Mac Rumours and other Mac threads, and also commenting on sites where a tech reviewer/commentator has reviewed IOS 9 and comments can be made?