SD cards that come with the generic Pixhawks are low quality. I normally replace them immediately with better brand ones, i.e. Sandisk, PNY, etc. Make sure you use at least a Class 4.
You can put a check mark on "Save telemetry log even if vehicle was not armed".
Click the icon with the Magnifying Glass the click Refresh to display available logs. Highlight the log you want then click Download.