There does appear to be something going on with older devices such as the iPhone 5s and the iPad Mini 2 that can cause crashing part way through a mission due to the limited resources on those devices. If you have one of those devices be sure to close as many other applications as you can before starting a mission to minimize this issue.
In the event of an app crash you shouldn't need to start all over again. If the app crashes, leave it off and push the RTH button to bring the aircraft in. Once you are on the ground you can open Map Pilot again and you the mission will still have the progress that has already been made and will pick up at the location the aircraft was in when the app crashed.