Glycolysis: The net ATP yield is 2 ATP. And, since NADH+H shuttles its electrons and protons to FAD, reducing FAD to FADH2, the net yield is 3 ATP in the ETC.
Conversion of pyruvate to ACOA: We do not produce any ATP in this stage. However, the 2 molecules of NADH+H+ will yied 5 ATP in the ETC.
TCA cycle: When calculating the total ATP in the TCA cycle, remember that there are TWO ACoA molecules. So, ATP is made one place in the TCA and with 2 turns of the cycle the ATP yield is 2. NAHD+H+ is produced 6 times (from the TWO ACOA) yielding 15 ATP in the ETC. A total of 2 FADH2 are yielded from the TWO ACOA, thus yielding 3 ATP.