Your MiniDisc charging capability is damage. If you know what to do, you can open up your MD and look for IC/transistor and diodes closer to the battery terminal connection and check for the fault, but finding a replace parts would be slim to none.
Otherwise find another way to charge the battery which probably better & cheaper than getting it fix. You might be able to configure a regular AA charger for your MD charger but it has to be out of the unit which is better than in the unit.
Charging habits is the main issue for any rechargeable batteries. Using the unit while charging increases current passing through the charging components which decrease its lifespan.