In Devangaryi nukta and halant are sometimes combined as nukta_halant to improve their combined appearance with some glyphs that lack a half form. When nukta_halant-deva exists Glyphs adds the following line to CCMP for the script dev2:
sub nukta-deva halant-deva by nukta_halant-deva;
This breaks rendering of consonants that include a nukta and have a half form. For example, ka-deva + nukta + halant + ka-deva should render as k-deva, with a nukta, + ka-deva. Instead it renders as ka-deva + nukta_halant + ka-deva. See images below, where nukta_halant is marked with a horizontal stroke to make it obvious.
This bug is present in both current versions of Glyphs 2, and I think it has probably been in Glyphs 2 since the beta period.