Incorrect math kerning algorithm
A char_node can only hold characters from 8-bit fonts; text from native fonts such as OpenType fonts are stored in either a native_word_node or a glyph_node, which are subtypes of the whatsit_node, distinguished by subtypes of 40 and 42, respectively. One would need a \lastnodesubtype to identify those. That might be a desirable extension.
Improvements to sub/superscript positioning in OpenType fonts
I had the same problem on Ubuntu 16.04 LTS with automake 1.15 and found a workaround...
Incorrect rendering of Vedic Sanskrit accents