Well you drive onto the train and you stay in your car and drive out. So yeah, you do drive a car there, the ground beneath you changes but you haven't really stopped driving.
The boroughs of NYC are unique in that they are counties, cities, and also part of NYC. Stating Brooklyn or Queens or w/e instead of NYC in the city column is allowed. So the cause is multiple authors of applications, not bad data.
Ahhh, ok, so along with @agilecoder comment above, this makes sense. If I have this right then nn LCA sounds similar to an LMO (Labor Market Opinion) in Canada, you need that to prove you are skilled, after which you can apply for the H1B visa.
Then the heading "Companies with the Most H1-B Visas" is misleading. It's a very poorly written/explained article IMO. Thanks for the clarifications.