Might be a forced discharge initiated. Leave the battery in the charger for a good while unless it gets very hot or starts to smell funny.
Li-Ion batteries never need to go though full discharge cycles, quite opposite, fully discharging them might damage them, and a good charger should then refuse to charge them. That is why the bodies have cutoffs listing them as "empty" (0%) well before they are completely discharged and reaches the very steep discharge curve towards zero voltage. Zero voltage can be very dangerous in multi-cell Li-Ion/Li-Polymer batteries if the charge is not properly balanced among cells, as it means that some cells get into reverse voltage where very bad things can happen.
A charger complaining could be problems with the built in chip, but also inability to balance the charge between the cells, for instance if one cell is going bad or the charge balancing circuitry is broken.
BTW, one sometimes sees questions if the new EN-EL15b batteries can be charged in the MH-25 (non-a) charger: I can confirm that my newly purchased EN-EL-15b (the only type that was available locally for my D500; vendors like B&H and Amazon refuse to ship them to Alaska) reaches 100% charge in both my MH-25 (non-a) and MH-25a charger. The first use of the EN-EL15b discharged down to 41% in the D500 before I recharged it again gave me 1367 frames, so with the same use (lots of high speed shooting) it can be extrapolated to 2317 frames for a discharge to 0% in that body.
I believe this was rather the result of the usage pattern (total on time), not the Li-Ion 20/a or -b battery type.
