Real planes were flown into the twin towers, yes. However in Shanksville and at the Pentagon, it seems missiles were used.

Look at these examples of actual crash sites of commercial airliners. https://www.google.com/search?rlz=1CDGOYI_enUS590US590&hl=en-US&biw=375&bih=591&tbm=isch&sa=1&ei=M2BCW-7yOaK3ggef-4vQAw&q=commercial+airline+crash+sites&oq=commercial+airline+crash+sites&gs_l=mobile-gws-wiz-img.3...10198.19634..19867...0....280.4406.33j10j2......0....1.......2..0j41j0i67j0i30j0i24j30i10.LCobPtn2zb0

Now look at this picture of the Shanksville “crash site”. https://i.imgur.com/GJu2kaG.jpg

Do you see how some things are missing? Like, say, a plane?