Try this, take a small slip of paper and fold it several times and put it into the charger bay such that the positive end of the battery is raised slightly. This will cause the battery positive terminal to make contact with the metal plate of the charger at a different point.
Somehow, the charger reads the battery as having a full charge if the positive battery terminal makes contact at certain points on the charger's metal contact. I've seen this issue with other chargers too. It happens regardless of the type of battery inserted, 18650,18350, AA, AAA, etc.
As for the safety of it, I'll let someone else chime in. My suggestion is only a temporary measure. I haven't found the cause for it. And yes, the metal contacts are clean.