Hyperlinks

For some reason when someone at the office I work at is converting  a document that has hyperlinks into a pdf through acrobat, acrobat adds hyperlinks in places there were not any, as well as adds hyperlinks over the existing hyperlinks. 

Is there a way to stop this or to scan a document after its converted to check for these errors. This will will become a big problem for us when we are converting 10’000 page documents into pdfs.