DJI Go is doing the recording of the log files. When you are using the Map Pilot app, DJI Go should be closed and therefore will not be recording any log files.
If you wan't to get the log data from flights made with the Map Pilot app, we have created an online viewer for the aircraft's internal data logger. This viewer provides both KML and CSV outputs.
These are not the same files that DJI's app provides but should do the trick.