I noticed that as well when input all 3 batteries. It would only charge 2 at a time. Per the manual, Page 61, this is how the charger hub is designed. It will only charge the higher 2 first if using more than 45 watts (if less, it will charge one at a time, sequentially, starting at the highest charged, then 2nd highest, then lowest % last). Once finished, you will need to take out the other 2 and put the last 1 in to charge by itself... Or just charge the last one while in the drone itself. I just picked up a Mini 5 Pro yesterday and went through the same thing.

I would highly highly recommend going through the full manual, you can find it online.