I just started a new model, and this seems to happen a lot. I'll extract faces for training, and then add faces while in manual, but the masking is off (covers too much area or not enough, and in some cases not at all) and the masking tool (not the alignment tool/box) won't let me edit the area.
Just to be clear, I'm not talking about the alignment box, I'm talking about the masking tool that covers the red area.
I'm not sure if this is a bug or not, or just a kink in the way it works.