I seriously doubt it's an app conflict. Third party Windows Phone apps simply are not able to replace or disrupt basic phone functions, unlike on Android devices. My guess is that you're encountering a defect ("bug") in the Wi-Fi Calling implementation on that phone.
A factory reset might help. I know it stinks to go through that, though. You can go to settings > backup to make sure that a lot of your customizations are backed up before you do the factory reset. More info here:
Learn about Windows Phone backup | Windows Phone How-to (United States)
If you do have cell tower access in the places where you use your phone, leave Wi-Fi Calling turned off.
T-Mobile has made improvements to the Wi-Fi Calling software that ships on the Lumia 635. I expect (this is just an educated guess) that these same improvements will be made available for us on the Lumia 521 and 925 devices in the next month or so. So at that time, hopefully your issue is resolved, but in the mean time you can try leaving WFC turned off (if that is ok in your area) or try the factory reset.