mark differences between fontmake and glyphs.app generated static fonts for NotoNaskhArabic

I haven't pushed these sources NotoNaskh-sources.zip nor these fonts to github because .... I get the following differences (look for some marks, not all, on top/bottom of other top/bottom marks) between the fonts generated by the glyphs.app (reddish) and fontmake (greenish -- this one has mark errors):

text for the above " لِيُنْذِرَ بَأْسًا الْكِتَابَ بَأْسًا اللَّهُ الْمُؤْمِنِينَ الَّذِينَ يَعْمَلُونَ أَنَّ بِهِ لِآبَائِهِمْ ۚ آثَارِهِمْ "

or (please look at some marks on the left of the greenish line)

text for the above " ٲُږّݳُݴُݵُݶُݸُݹُݺُݻُݽُݯُ ڕِݕِݼِݷِݚِࢠۭࢳِ "

Do we have a source problem (if yes how to fix it)? fontmake problem? or some library problem?

fontmake generated fonts are here: NotoNaskh.zip

glyphs.app generated fonts are here NotoNaskh-glyphs-generated.zip

does fontmake have any problems with marks on top/bottom of other top/bottom marks? If yeas, how to overcome it?

Any help would be appreciated