Glyphs seems to have a similar issue like the one I reported in Fontlab a few years ago: one handle is lagging behind when nudging. It seems to occur on paths including missing extrema (that are however at least one node away from the affected area, which seems strange).
nudge-bug.glyphs (4.8 KB)
Are you nudging with Option pressed down? Then this is the intended behaviour for handles that you don’t select.
And why didn’t you select those two offcurve nodes?
Oh. I see. There are indeed unselected handles, and why is that, I have no idea. All good.