You need to use a newer fontloader. Please try the experimental luaotfload:
With it (the patched one) everything seems fine, and the babel samples in GitHub are rendered as expected ( https://github.com/latex3/latex2e/tree/master/required/babel/samples ) with Amiri, FreeSerif, and Arabic Typesetting, but I'm still doing some tests (well, Amiri has some problems, but they are unrelated - the point is the letters aren't misplaced). Javier
