The CF-1040 appears to be a "common" form for cities in Michigan. Oddly, I can't find such a form on the state's website. However, Battle Creek certainly wants taxes (see this Battle Creek page).
Sometimes versions of our Online and desktop products get out of sync and don't update properly. However, it is likely that the form used in our product has the same boxes and descriptions as the real form, which means everything is fine.
Note that what we e-file is not the PDF that you see, but a format called XML which does not contain any graphical elements like lines or boxes or fixed text. If your return was Accepted by the state, then the XML version was fine, as far as the state is concerned.
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