So basically the behavior is "correct" in your case. You have the directory entries .dovecot.sieve and .subscriptions, which is anyway a directory indeed, so that's not even a bug. Move all your maildirs to /home/mail/%d/%u/Maildir and then update mail_location accordingly. Then move out the sieve files - .dovecot.sieve, sieve/, .dovecot.sieve.log, .dovecot.svbin to the home directory.
It looks like these are not system users, so you may need to set mail_home explicitly to set up the home directory to /home/mail/%d/%u
I was not saying it was a bug, was just asking for some advice on this :)
But yes, I've read this some times but didn't noticed the end of the mail_location. Understood and thanks for this!
I still have only a few users so I can convert them, as I don't want to use the below option:
maildir_stat_dirs = no
Thanks for your help,