Yes, that is a description of a short circuit which should have destroyed the batteries. Unless one was dead, or, hopefully, one of the wires acted as a fuse and is now just two dead ends.
Parallel is black to black, red to red, red to ESC pos, black to ESC neg. Nominal 6 volts, longer run time at lower speed.
Series is Battery A red to Battery B black, Battery A Black to ESC Black, Battery B red to ESC red. Nomnal 12 volts, higher power, shorter run time.
As Tug-Kenny said, test each battery separately. Then test under load. There should be no significant difference, such a difference with either means that that battery is in poor condition.