The quad kept climbing because its altitude estimate was bad. The GPS altitude and the fused estimation never moved significantly, only the barometric height shows the climb.
The GPS Uncertainty plot shows a vertical (and horizontal) accuracy of about 10m, and the GPS fix degraded. So indeed the GPS data wasn’t very reliable. Also, you have some timeout flags in the watchdog, but I don’t know the exact meaning of them. I could imagine they are linked to your bad position estimate. Is this the first time that you experience problems with the GPS?
I have also noticed that you are using the LPE estimator, which is no longer maintained. Have you considered switching to EKF2?
I don’t know anything about LPE, but with EKF2 you could choose the primary height data from the barometric sensor if the GPS keeps being unreliable. Also, there are preflight checks on the position error and minimum satellite counts that prevent arming when the position estimate is too bad.
Hope that helps,