If you're getting notifications for reminders and timers that have already been completed, postponed, deferred, you are experiencing an iOS bug where notifications get stuck after an app update or iOS update.
The only resolution is to restart your iOS device. To do so press and hold the Sleep/Wake button at the top (iPhone 5s or earlier) or right side (iPhone 6 and iPad) of your device until a red slider appears on screen. Slide your finger across the slider to turn your device off.
After the screen becomes completely black, turn your device on again by pressing and holding the Sleep/Wake button until the Apple logo appears.
You may have to launch Due after your device restart for these phantom notifications to be fully cancelled.
I've filed a bug report with Apple about this problem and hopefully they can fix the problem soon.