Hello Crissa.
It sounds like you're experiencing problems with your Phone app notification badge not clearing unless you manually delete the missed calls from the Missed calls list. I can definitely understand how cumbersome this could become if you typically receive a lot of missed calls. What you're experiencing is actually not expected behavior. Typically with the iPhone Phone app, no matter how high the number is for the Phone notification badge, the badge itself should disappear once you open the app and select the Recent tab. This should occur without you having to manually delete each one of your missed calls. Since this isn't happening on your iPhone, let’s try some steps to see if we can get it working properly.
Due to the nature of your issue, and because of possible steps we may have to take to get a final resolution, we recommend creating a backup of your iPhone data first. If you're unfamiliar with how to back up, you can find the exact steps in the following support article:
How to back up your iPhone, iPad, and iPod touch
Next, make sure you're running the most up-to-date iOS version. The most current iOS version is 9.3.4. You can view which version you're using in Settings > General > About. Keeping your phone up to date ensures that it will run as smoothy as possible. In addition, updates can provide fixes for issues like the one you're experiencing. For steps on how to update, use the following support article:
Update the iOS software on your iPhone, iPad, or iPod touch
After updating, test out your iPhone to see if you're still experiencing the same issue. If you're already running the most recent iOS version, the next step would be to force quit the Phone app and then restart your iPhone. You will find steps on how to force close your Phone app and restart your iPhone below.
Force an app to close on your iPhone, iPad, or iPod touch
How to restart
- Press and hold the Sleep/Wake button until the red slider appears.
- Drag the slider to turn your device completely off.
- After the device turns off, press and hold the Sleep/Wake button again until you see the Apple logo.
Restart your iPhone, iPad, or iPod touch
Test out your iPhone once it's restarted. If the issue persists, the next step would be to reset all settings on your iPhone. Resetting the settings will not erase any of your actual data from your device, however, it's going to set certain software settings back to default. This includes things like, sounds, Do Not Disturb, wallpaper, Wi-Fi passwords, and VPN/APN settings. Complete the reset by going to Settings > General > Reset > Reset All Settings. Test out your iPhone after the reset is complete.
Thanks for using Apple Support Communities.
Take care!