I'm not sure but maybe some errors occurred during the pdf to epub conversion. It happens when you use calibre. Actually no pdf conversion software is error free.
Try this- convert the pdf file to html and fix all the errors manually(remove any headers or footers, and fix any broken paragraphs, eliminate hard line endings etc.). Then convert it to epub.
you can also try pdf to mobi to epub.
It's quite hectic. Frankly pdf is the worst source format that you can use. You're guaranteed to get errors with automatic conversions.