If the app crashes (on e.g. startup) on update/install where the user is presented the "enable notifications" button, the app will assume that the user accepted notifications, and it will be enabled in the apps settings, but not when navigating to the devices settings.
This happened to me. I had updated the app to build 961, I went through the 'First Time Experience'. Then instead of pressing the message about notifications, I scrolled down, then up again. The enable notifications message was gone, but then the app crashed. And subsequantly crashed on startup (when trying to access the explore feed). This caused me to have never recived a single notification. After having updated the app a few times to newer builds, I checked the apps settings and notifications was "toggled on" there, but when navigating to the iPhone/iOS-settings, the WIkipedia app wasn't even listed under the possible apps for notifications. I uninstalled the app and installed it again, went through the FTUE (first-time-uer-experince) and enabled notifications.
iOS 10.1
iPhone 6s
Build with the crasher: 961
Build after uninstall: 993