This forum is for reporting errors with the Extraction process. If you want to get tips, or better understand the Extract process, then you should look in the Extract Discussion forum.
Please mark any answers that fixed your problems so others can find the solutions.
Jus to add, this only seems to be an issue for newly extracted data.
The Manual tool works on older (last week) alignments. I can also extract facesets from both old and new alignments, however connot run the Manual tool on the new alignments and source data.
I narrowed this down to a sequence of editing with IOS software, seemed after some touching up those specific images wouldn't work. Haven't been able to replicate so don't think will be an issue that needs a fix or that will cause problems for anyone else.