I think this is a mark propagation issue. Take the string صَىَ ضَىَ صَ ضَ and AlYamama:

With the TTF (correct):

With the .glyphs file:

The glyph with dot is a composite glyph in both cases, when it is a single glyph the anchor gets propagated from the dot as expected, but when it is a ligature the anchor does not. Or may be the anchor is propagated from the dot but not converted into a ligature anchor.