They're not stacked, they're just plotted on top of each other because there's only one series on each call to bar(); hence there's nothing to group. You just see whichever is the taller and if it happens to be the RH axis that is the top layer, then you see both which gives the appearance of stacked--but you'll note the value isn't the total as would be for a real stacked bar.
A diagnostic warning message about using the 'stacked' option with only one series might be a useful enhancement to give the user a clue what's going on.
Try
yyaxis left
bar(t,[a nan(size(a))],'grouped')
yyaxis right
bar(t,[nan(size(b)) b],'grouped')
The "trick" of a NaN placeholder array is a very common one and is often necessary to get the desired result with handle graphics as here.
