What version of InDesign? Older versions of InDesign had a bug where with some characters URLs where cut off upon PDF export.
Did you write the URLs into the Hyperlink Panel or does Acrobat read it from the text?
Indesign CC for the Mac. The curious thing, is that when you hover over the url, the whole url shows up, but you can not access it unless you click the first or second line.
What PDF reader are you using?