Probably because you were in a large aluminium tube at the time, and had no internet to get the AGPS data, so it had to receive the orbital elements from the satellites. (IIRC, this can take as many as 24 minutes worst case)

If you're using GNSS tracking on a flight, consider checking out the OSMand~ app for android. There's a map layout for flying, though I don't know if the navigation features work.

Civilian planes do not go 1000kts or up to 60,000'. Your phone GPS works fine in a plane as long as it can see enough satellites (pick a window seat).