You must be using a really old copy of GeoTools - I have not seen the filter.and(filter2) use since we made the filter interfaces immutable in GeoTools 2.3?
Can you try setting this up using filter factory all the way:
filter = ff.and(
ff.greater( ff.property("Shape_Area"), ff.literal(100000)),
ff.equal( ff.property("CITY"), ff.literal("ANKARA"));
Or using CQL:
filter = CQL.toFilter(" Shape_Area > 100000 AND CITY = 'ANKARA'")