'out of place' can mean several things, but here it means 'incorrect' or 'wrong' "The formatting of the word file is incorrect/wrong." It's saying that the formatting that you expected is not there. Perhaps the paragraphing is wrong or missing, perhaps the wrong font style was chosen, perhaps the file is almost unreadable because of incorrect font characters/missing spaces. There are many possibilities.

It means that it is either in the wrong order or incorrect. Maybe you could say the formatting of the world file is incorrect due to.....