It is not a first time with similar problems in smartphones. In this case, as there is no visible damages to the battery, I am suspecting that USB plug was not fitted in socket correctly, and electric contact was not perfect or there was some dirt on contacts (and some series resistance caused additional heat dissipated during high current charging process).
I am not saying that it is userís fault. Not. Problem is that micro USB port (enforced by some eco bureaucrats as charging standard) design is not so great for currents up to 2A.
Samsung should put additional temp sensor chip (not only sensor alone, but supervising chip, independent from OS running fine or not, which would be able to shutdown phone) very close to the USB socket.
Safety regulators should enforce such requirements and respective certification tests. Many vendors sometimes demonstrates their scratch tests, endurance testing, super duper audio bits, camera test etc. but I never heard about advertising of safety/temperature/fire tests...
My advice to you is to take high quality high resolution photos (better then these on dropbox) of battery, charger and cable, before you ship phone to the Samsung. Just in case, to avoid to hear next month, that it is your fault because you used fake/unauthorized battery/charger/cable.