the problem here is that the LVS should filter the devices which are connected as dummies. Please paster the following command in your rule deck for eliminating dummies.
FILTER-LAY-OPT = options...
where options are B,BA,C,D,E,F,H,I,J,K,L,M,N,O,P.
The options are for eliminating dummies where gates are connected to gnd, where sources and drains are connected together, where sources and drains are connected to gnd or to power supplies and so on.
I hope that this helps