This usually means that there is an error in the epub. While the calibre viewer is a good reader, it is very forgiving of errors in books. The Kobo firmware is not. Things like unbalanced tags can cause problems like this. I recommend opening the epub in the calibre editor and running the error check on it. If there is an error, this will probably show.
An alternative reason is that you have installed the KoboTouchExtended driver and sent the book as a kepub. And enabled the full screen reading on the device. The full screen reading is an unsupported function on the device and suffers from problems with text going over the edge of the screen.
Other than that, I would need to see the book, or at least a sample, to see what is wrong. .
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