An interesting thread...
I used to work on charging systems for digital camera and did intensive study on different battery chemistries - as we were designing in camera battery chargers the accepts multi-chemistry AA batteries and also dedicated square battery packs for slim cameras.
On the part of the lithium Ion batteries, they are usually voltage level sensed on chip. Once the voltage level across the battery terminal is reached, then the current pumping will cease.
Problems will comes when you have resistances along the path like bad contacts, oxidised contacts(resistances) that might just "reflect" wrong true battery level which then shut off the voltage prematurely - notice the amount of work done on battery contacts design to intentionally scratch the surface off the"oxidation".
So you will get batteries that are not getting full charge even when battery chargers stops charging the Li-Ions.
So best is to keep the contacts clean and "rust" free.