Actually it is a Hollywood mock-up (same as the Tiger I based on a T-34 chassis in Saving Private Ryan) of one of the Horton Brothers early attempts at producing a "flying wing". It is similar in design but not identical. Also, another point worth mentioning is that the Horton Bros. had not yet been contracted by the Luftwaffe to produce this peticular aircraft at the stage of war which is depicted in the film. So in technicality the aircraft should not have been there in the first place! Hope this helps with the confusion!
I don't think this is a big mistake. I agree that such planes did not exist, at least not in sufficient production quantities. I don't mind that. The plane looked like it could have existed, and it added to the story. My opinion is based on an interview with Steven Speilberg (I think it was him, maybe it was George Lucas.) He said the flying wing was in the movie because he always wanted to make a movie with flying wing.
It looks an awful lot like a 265, but it isn't. The 265 had a single vertical stabilizer, whereas the plane on the film has two. It also has the gun turrett, which the 265 didn't have. Good observation, though.
I don't know all the makes and models of American flying wing designs and German designs (both real and the ones on the drawing board at the time (so-called Luft '46 designs)), but in my opinion the Flying Wing in Raiders of the Lost Ark looks most like an Arado E-555. The most striking differences are that the tail guns at the very back of an E-555 are (were supposed to be) remote control (the one behind the flight deck looks like the one in the movie plane), and of course that the E-555 is (was uspposed to be) jet powered. Actually there were 15 (or so) Arado designs of the flying wing, but the most popular version had jets... refer to Revell's 1/72 scale model which is no longer available but very cool; you can find it on E-Bay (sometimes). Check out how the nose of the E-555 looks like the Millennium Falcon... George Lucas must have really loved this design!