Basically, the only way they could avoid that is to have everything in focus, which looks very weird and fake in 2D. It's a tradeoff- you either have it look perfect in 3D, or you have it look nice in both, and have to deal with those issues. After the first 10 minutes or so, I found that if I let my eyes follow the focus line, the movie placed everything where it needed to be in terms of focusing. After that, I had no problems with it. You just have to train your eyes not to focus on stuff in the foreground.
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