They can deny you for any reason. Very literally any reason. It's not newsworthy, they've been able to do this since the US started to control immigration and it is not related to what the NSA has been doing since basically the NSA has been in existence.
People are trying so hard to find tangible evidence of someone doing something with info the NSA has collected that they are latching on to anything that could be construed as such if you look at it believing you found that evidence.
It's almost like that example Doctorow gave about false positives when you're searching for very rare events... now HN is "flagging" every government screw-up involving non-Americans as being due to PRISM.
People are trying so hard to find tangible evidence of someone doing something with info the NSA has collected that they are latching on to anything that could be construed as such if you look at it believing you found that evidence.