I have come across this in a large number of transistors.... mostly to do with the SOT23 footprint. I am not sure if the problem lies with the schematic pin numbering or the footprint numbering. It has happened so often I now double check all transistor footpint connections and correct accordingly there and then.
My golden rule is ... if its a transistor-check the damn thing !
Make sure that you do NOT have demolib.psl installed. If you DO have it installed, delete the SOT23 footprint from it. That's the one with the wrong pinout. We haven't shipped it since V11, but a lot of systems still have it as a legacy file, and as it's early in the alphabet, it's often picked up in error.
As far as we're aware, that's the only faulty footprint in the standard libraries.