listA = [[a,b,a,b,c],[c,f,q,a],[a,b,c,d,a,a]]
listB = [[a,b],[c,f],[a]]
test = [i for i, enumerate(listB) for items not in (listA)]
desired_output_indices = [[4],[2,3],[1,2,3]]
It's a bit trickier than you thought:
[[idx for idx, elt in enumerate(sublists[0]) if elt not in sublists[1]]
for sublists in zip(listA, listB)]