More specfically, FADH2 doesn't create 3 ATP because its redox potential is only slightly lower than the complex in the ETC where the electrons from FADH2 enters (Complex II).
Remember that the complexes in the ETC go from more negative to more positive Redox potential as you move further down the line. This change in redox potential is why the ETC can generate an H+ gradient for ATP.
So the electrons from NADH travel from NADH --> I --> III --> IV, which is three increases in redox potential (from NADH to I, then I to III, and III to IV)so 3 ATP are created. (This is very simplified to make it MCAT relevant).
The electrons from FADH2, however, Go from FADH --> Complex II --> Complex III --> Complex IV. In this progression there are only 2 increases in redox potential (from II to III, and III to IV). The change in redox potential between FADH2 and Complex II isn't large enough to translocate H+ to the IMS. Thus, there are only 2 ATP produced.
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