I do have a little in-app banner at the top of the logbook screen for messaging like prompting to create an account, or upselling premium, or other things. It has grey background, but its buttons are blue and it has a red dot on it so it doesn't look to clone the appearance of a system notification perfectly or anything (it isn't even pinned to the top of the screen or anything, where notifications come from). Maybe you thought it was a notification? But it can only occur in-app, on one screen, and is in no way a violation of Apple's ToS.
Edit: Screenshot of the in-app banner to aid discussion: https://www.dropbox.com/s/i3ib5pbfg5eid51/Screen%20Shot%2020...
Edit 2: The banner used to be all blue, which looked even less like a system notification, but I was worried it was too distracting from users' content so this season I opted for a grey background to help it blend in more.