Towards the end of the scene when Gibbs confronts Quinn at the hotel bar in Philadelphia, she takes a sip of her drink and we can see she has just enough liquid left to cover the bottom of the inside of the glass. However, on her next sip moments later, she now has almost a quarter of the glass filled with liquid.
Upper Darby is characterized as being "20 miles" outside Philadelphia, and the victim was planning to take the train home. Upper Darby is basically adjacent to the city, and he would have taken the Market Street EL and a bus or trolley.
During the flashback of Alex's old Philadelphia partner "Philadelphia" Port Authority Emily, their car had a front Pennsylvania plate. Pennsylvania only issues back plates. Also it's not the Philadelphia Port Authority, it is the Delaware River Port Authority.
They said the auto shop was in East Falls - bad location to begin with since East Falls doesn't have those kind of businesses - but then Bishop refers to it as "East Bay".