As per my comment, I raised a service request with Mathworks and they have confirmed that it is indeed a bug.
As the bug is not present when 'ByRows' is false (the default), they recommend to use:
all(ismembertol(aa, bb), 2)
ismembertol(aa, bb, 'ByRows', true)
This works as long as you don't need LocB. If you do need LocB, then I recommend you remove the NaNs from the arrays.