I assume these markups are to PDF documents? Have you tried using Adobe Reader and if so does it happen there? Are all these documents from the same source?
Preview has, from the very beginning, had various problems with a few PDF documents. Sometimes it is because there is a PDF function used in the document that is not in the public domain and therefore not supported by Preview. Sometimes the application used to create the PDF is creating some slightly wonky code as far as Preview is concerned. Very rarely, not even Adobe Reader will react correctly with a given document. Preview doesn't fail/glitch often with PDF, but it has happened to me enough times that I no longer use it with PDF documents.
