The most likely answer, I’m afraid, is that you did something wrong, or failed to understand how Word works and ended up “breaking” the document layout. This very rarely happens on its own. The most common reasons for “WTF? Why did my document layout change? Word is such a terrible program!!” include. Users deleting a Section break and then acting all surprised when the formatting of the section following the section break is now applied to the entire document. Well duh… That is the way it works. Before you start messing with Section Breaks, try to learn about what t are. Hint. A Section Break is a VERY different thing from a page break. Users opening a Word document on a machine that doesn’t have a needed font installed (or whose special fonts are licence-protected and cannot be embedded). Or with the required fonts simply not having been embedded. Well duh again… Of course your document is going to look different if you’re not using the correct font, because Office substitutes missing fonts with a standard font that it feels “looks right”. But sometimes it is so different that the result is almost comical. Users not understanding that Styles can refer to one another, and changing one style will also apply that change to all other styles which based upon said style. So yeah. That’s actually by design. But if you don’t know what you’re doing, you are going to be surprised (horrified?) by the changes “stupid Word” makes when you screw with a formatting style. Yes, if you change the paper size of a document, then the layout WILL change, unless you have been very careful how you define things like table width and so on. That’s how it works. And so on. So usually, it’s something you (inadvertently) did.
The PDF's OCR has limitations which are usually pretty subtle, such as not being able to distinguish between different types of fonts (which is why I'd go with a monospaced font and make sure that I had the same one in my document too), and that will happen more often than it should with any image file.