I found a setup that triggers it again (often but not always happening).

Once reproducible I took backtraces of the sys open to see what in ntp
does that.

Both opens are from the same place.
Thread 1 "ntpd" hit Catchpoint 1 (returned from syscall open), 
0x00007f8afd8fcd53 in __opendir (name=0x7ffc9999df90 "/usr/local/sbin")
    at ../sysdeps/posix/opendir.c:191
191     in ../sysdeps/posix/opendir.c
(gdb) bt
#0  0x00007f8afd8fcd53 in __opendir (name=0x7ffc9999df90 "/usr/local/sbin") at 
../sysdeps/posix/opendir.c:191
#1  0x00007f8afe5c6ba7 in ?? () from /usr/lib/x86_64-linux-gnu/libopts.so.25
#2  0x00007f8afe5cdde6 in ?? () from /usr/lib/x86_64-linux-gnu/libopts.so.25
#3  0x00007f8afe5cfa4f in optionProcess () from 
/usr/lib/x86_64-linux-gnu/libopts.so.25
#4  0x000055c12781ae7f in parse_cmdline_opts (pargc=0x7ffc9999f0dc, 
pargv=0x7ffc9999f0d0) at ntpd.c:359
#5  0x000055c12781af8d in ntpdmain (argc=<optimized out>, argv=<optimized out>) 
at ntpd.c:575
#6  0x00007f8afd84a1c1 in __libc_start_main (main=0x55c12780b0e0 <main>, 
argc=8, argv=0x7ffc9999f6b8, init=<optimized out>, 
    fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7ffc9999f6a8) 
at ../csu/libc-start.c:308
#7  0x000055c12780b11a in _start ()

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https://bugs.launchpad.net/bugs/1741227

Title:
  apparmor denial to several paths to binaries

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