Most likely your speed at 5m/s combined with your photo settings is not a suitable combo, and the camera is not able to take photos at each waypoint as it’s still busy writing the previous shot to sdcard.
Things that can help:
reduce speed
set Photo format to JPEG only
set Resolution to 12MP (Litchi Hub uses 12MP for mapping calculations)
For 2. that’s strange, perhaps the mini 5 pro kept taking the queued photos that were not taken during the actual flight?
I have also experienced this with a Mini 5 Pro. If a waypoint mission configuration includes a photo at every waypoint (separated by a relatively small distance) and the flight speed is greater than what will be needed to capture those photos, the drone seems to queue the capture photo actions up and execute them as fast as it can even though those actions may occur later in the mission or even after it completes.
This is an unfortunate implementation by DJI. As Vico says, the only way to prevent this is to reduce the speed, allowing the drone time to capture each photo at its desired location. In some cases, I have to set the speed to less than 1 m/s for waypoints that are close to the minimum distance apart.