This appears to be being triggered because there are actually two independent profile parsers in apparmor. There is a C version used by the apparmor_parse which correctly interprets the 'include "xxx"' syntax and then loads the profile. There is also a python parser (in aa.py) which only seems to understand the 'include <xxx>' syntax and it is this which throws errors when running the utility commands.
This appears to be being triggered because there are actually two independent profile parsers in apparmor. There is a C version used by the apparmor_parse which correctly interprets the 'include "xxx"' syntax and then loads the profile. There is also a python parser (in aa.py) which only seems to understand the 'include <xxx>' syntax and it is this which throws errors when running the utility commands.