GPS works by computing your distance from satellites by measuring how long it takes radio signals from those satellite to reach you. As an electromagnetic wave, radio moves at a different speed through plasma (which is full of charged particles) than through holes in that plasma, so this will change how long those radio signals take to reach you, which will change how far away from the satellite you think you are.

Ionosphere's charge density introduces change in speed of the radio waves passing through it. This messes up with the GPS' calculations which assumes that ionosphere's density doesn't changes rapidly.