It's happening here with an iPhone 6+ and 9.0.1 (13A404)
Of interest, I used Due to set a reminder to go off every minute, then I launched a few other apps (Safari, Mail, Photos, Slack) and then shut the phone off. Then I let it sit in front of me while I worked.
The first ten or eleven notifications came in without issue. After that it was about 50/50. Every minute the notification center item appeared without fail, but the sound failed intermittently. I then began sending myself notifications in Slack, Messages and Tweetbot. Sounds for these failed intermittently as well.
I tried again with the phone powered on the whole time, and with it docked versus undocked. None of these made any difference. The first run of notifications were fine, then they began to fail.