Bogdanovich explains this on the commentary track (Chapter 26):
"In some scenes - it's noticeable particularly in the funhouse scene, in the mirror scene at the end, but there are other places where you can see it - he actually changed the aperture in the camera when he shot, so that sometimes the image was narrower than normal, top and bottom. He did that on purpose in a way that in fact DW Griffith did, changing the shape of the image by masking the top and bottom or the sides or whatever, something that Griffith did. Orson brought that into sound pictures, something that very few people did. He was amused that he'd done it and nobody'd ever noticed it."
On the DVD, the shots of Michael stumbling through the crazy house are about 1.17:1 (like early synchronised sound films, eg Sunrise, M, The Public Enemy, though this last one is not presented in the correct ratio on the Warners DVD), then back to 1.37:1 for the shot/reverse shot of Elsa shining a torch in Michael's face and entering the mirror maze, then a switch to about 1.66.1 for the first shot of her with mirrors, then back to 1.37 for a reprise of the previous shot as Michael enters, and then much of the mirror maze stuff is 1.66, but with occasional 1.37 shots appearing (eg Bannister in three mirrors moving right to left, medium close-up of Elsa pointing gun directly at camera, insert of a hand switching on the light). In the later part of the shootout there are also shots that appear to have been filmed in 1.66 but then had broken glass effects superimposed in 1.37 (eg Bannister firing directly at camera), as well as shots with the superimposed glass in 1.66 (most noticeable when the camera pans right as Elsa exits the mirror maze and broken glass effect pans with it!). The scene with Michael and the dying Elsa continues in 1.66 (including a cut back to Bannister as he dies) until a cut to a high angle of Michael exiting the turnstile in 1.37, followed by a reprise of Elsa in 1.66 as she dies, then a dissolve to Michael outside for the final track and crane.
I think it's safe to say this sequence shows signs of the film's complicated production history. Famously, the part of Michael in the crazy house was originally much longer, and presumably was all shot in 1.17. While a lot of the mirror maze scene was apparently done "in camera" (particularly up to Bannister's entrance), various superimpositions were done in postproduction, most noticeably the closeup of Bannister saying, "Of course, killing you is killing myself...", with a still image of Elsa on the right (probably a blownup detail of a single frame from elsewhere). At some stage superimposed effects of broken glass were added to certain shots. And it looks as if some additional shots were made after principal shooting had ended.
Obviously the fast cutting of the sequence means a lot of this goes unnoticed. What's much more jarring is the cutting into what was presumably a sustained low-angle shot of Elsa on the floor dying, with Michael in the background. This is interrupted by a cut back to the shot of Bannister as he dies, but when we return to Elsa, Michael (who was in the back left corner) now appears from screen right, suggesting a significant part of the shot has been removed. And the closeup of Michael exiting the turnstile is obviously in the wrong place, as on either side of it he's still inside with Elsa. Presumably it was supposed to follow the end of the low-angle shot which now comes immediately after it.
While it's impossible to know which elements of all this were supervised by Welles and which happened in the year or so between his stopping work on it and its eventual release, some parts at least are very clumsy. Apparently James Naremore's bookThe Magic World of Orson Welles has a discussion of what the film was like in its prerelease form. Anyone got a copy?