It could be a number of things that cause it not to pass.  Many places
do a visual inspection and if the complete smog system from the factory
isn't on the engine it will fail no matter what the tail pipe sniffer
reads.  Anybody thinking of buying any car with a modified engine should
consider emissions requirements.  Otherwise, the car may be sitting in
the driveway if they can't afford to bring it into specification.  The
car may not even have catalytic converters on it for all we know.

Here in Virginia some counties don't require any emissions but in, and
around, the metropolitan areas there are very strict regulations and
testing required every two years.  If someone buys a vehicle in a
non-regulated county and tries to license it in a regulated one they
might be in for one hell of an expensive surprise.  In my county, in
addition to testing the tail pipe emissions, there is a visual
inspection and these inspection guys know what the factory smog system
consists of and expect it to be on the engine. Also, all these tests are
tied into the State's licensing system so the guy doing the testing
can't screw with the results unless he is a serious computer geek and I
doubt many of them are testing cars for emission compliance.