Look carefully you might have a variant with the same option, you can check it out by looking at the master variant detail page, in the list of variants you see in the option Column multiple rows with the same segment and option:
in the picture OPZIONI stands for OPTIONS and "colore: Turchese" "colore: Giallo" for Segment and Option
i happaned to have rows with the same option, and when you try to update any other variant of the same products you get that error