I have the Mini 2 Fly More Combo and thus have the triple charger.
A strange thing happens randomly in the 10 months I have had it. I go out and fly… come back having used perhaps two of the three batteries… the charger finds the lowest charged battery and start the re-charge in that order… yesterday, again, one battery flashed just two LEDs and no charging… I took it out and it charged the other used one, normally.
Strangely when this happens i just put to offending battery in the Mini 2 to charge it internally and it charges perfectly.
This happens once or twice in three months… not a real problem as I can still use all of my batteries… it is just strange.
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How cold are the batteries? I’m sure you get two flashes of LED to indicate they are too cold, that has happened to me a couple of times if I have left them in the van overnight.
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Warm battery’s after flying can give flashing lights
interesting comments: thanks for replying @mynameisjoe and @Sparkyws … too hot or too cold… yesterday I had some roof repairs and inspected it all after the builder left… I had not charged up the battery from the last long flight but it was only a 5 minute flight. was cool and i had a battery low warning.
I didn’t recharge that cell till a bit later though and in a warm house… why charge ok in the drone though?
as I have said it is not critical… just strange.
You got there just before me dammit! 
The charging hub will have much more complicated charging circuitry inside it, allowing it to see the temp of batteries. The drone won’t.
It was exactly the same as the situation I had, hub wouldn’t charge the batteries but the drone would. Once they had warmed up in the house for an hour they charged up fine.
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Great information @mynameisjoe and @Sparkyws
I’ll make a better note of the flashing and LEDs next time and refer to the chart
Great forum and friends
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Just on a different train of thought from the temperature thing, are you putting the same battery in the same charging pod every time? Most of us have probably labelled the batteries 1, 2 & 3 and labelled the pods 1, 2 & 3. Do you still get the same issue if you swap to a different pod?
The labelling of the batteries and pod slots is maybe not as common as I think but I like order 
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you sound like me…
but although I have numbered the batteries I don’t tend to put them in an order in the charger
I must save this well done that man I tip my hat to you , 
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Numbered the charger slots and batteries the day I got my mini 2 fly more combo, have yet to use all three batteries in a day and never put them in the charger straight out of the drone, I always let them cool off first. However you should keep them in the charger, when not being used, even if the charger is not plugged in, otherwise they will not discharge properly, which is necessary for proper battery longevity and health. Batteries will charge in order from least used to most used and even if you never used one of the three, when you eventually plug the charger in, the unused battery will charge fully, as even a fully charged battery, will slowly discharge and that is perfectly normal. NEVER keep a battery in a fully charged or fully discharge state. It can cause damage and drastically shorten the life of the battery.
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I’m glad you are asking these questions as its great reading and saves me posting the same questions 
The batteries will discharge properly wherever they are. It didn’t use to be the case, for a long time they did not discharge properly when in the combo charger and had to be stored out of it, or use 3D printed widgets that fit between battery and case to stop the battery contacting the case.
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