Neurological adaptations, style of training, level of muscle mass.
For instance -
You can have an individual who is more muscular, trains specifically in the bench press and has short arms and another individual who is less muscular, doesn't train bench press that much and has longer arms. However, the latter individual is stronger genetically (more neurologically efficient in high intensity exercise) so, he can bench press more. This is the reason you can see a lot of small guys with huge lifts. Not the most common case, though.
Another case -
You can have two individuals who are virtually the same, one with long arms and one with the short. The only other difference is the the long armed individual trains the bench press specifically, so he has undergone the neurological adaptions to become stronger in the lift. The short armed guy, who in theory should be the stronger lifter because of his superior leverage, is weaker in the lift because he doesn't train it specifically.