Do you need something along this line?
% - Build small test case.
A = sprand( 4, 5, 0.5 ) > 0 ; % 4x5 sparse.
B = sprand( 4, 4, 0.5 ) > 0 ; % 4x4 sparse.
% - Find intersect of matching locations of non-zero elements.
[A_r, A_c] = find( A ) ;
[B_r, B_c] = find( B ) ;
matching_rc = intersect( [A_r,A_c], [B_r,B_c], 'rows' )
Which outputs e.g.:
>> A
A =
4×5 sparse logical array
(4,1) 1
(1,2) 1
(1,3) 1
(2,3) 1
(4,4) 1
(1,5) 1
(2,5) 1
>> B
B =
4×4 sparse logical array
(2,1) 1
(4,1) 1
(2,2) 1
(4,2) 1
(1,4) 1
(2,4) 1
(4,4) 1
>> matching_rc
matching_rc =
4 1
4 4
