Just joined the forum looking for info on another issue and noticed this subject and would like to offer some input.
We bought our 2012 1.6 auto Zetec last June with 10,000 miles on the clock.
Loved the car and had no issues until the end of August. Then the battery light started to make the occasional appearance. Checked the fan belt and as the light never stayed on for long, never thought anything about it.
Coming into the autumn, the light was appearing more and more. Plus, we discovered that the heated window didn't work work when it was on.
A service was due and we asked them to check out the battery light.
The local Ford dealer decided that the battery was faulty and needed to be replaced. It was out of warranty, of course.
Sooo, wallet lighter by £120 off we went. Didn't fix it.
They tried a few things and were talking about replacing the wiring harness!
Turned out(they said) that the firmware in the ECU had to be upgraded with a new program from Ford.
This was mid October and, touch wood, no more problems. Oh, got our money back on the battery.
Never flattened the battery but might be worth mentioning. Sounds similar.