The answer is YES. Let G=SL(2,3). Then |G|=24 and G has a normal subgroup H of order 2. So the quotient group G/H is a group of order 12. However, G has no subgroup of that order.
So the structure of a finite group really depends on the chief factors, not only the subgroups.
Now a dual question arise, that is " Does there exist a group G with a nontrivial proper subgroup K, such that K is not isomorphic to a quotient of G? "
but about this question obviously we can put G=A_5 , the simple alternating group
and let K to be a subgroup of order 2. Then G has no a quotient isomorphic to K.
In symmetric group S_3 , there is a normal subgroup K={e, (123), (132)} of order 3. But there is no normal subgroup H of order 2, so K is not isomorphic to a quotient of G.