I have a possible explanation for this seemingly incongruity.
At the end of the 1940s flashback, we see Joe put the butterfly in the wall. What if when Vera leaves the Pennybaker club, she leaves through the back of the club and the back entrance is down in the basement.
Stan of course parks in the front of the club, goes down into the basement to the back of the club, finds the butterfly, comes back up into the main part of the club and gets killed which is witnessed by pretentious treasure hunter guy.
Of course, this begs the question of why Stan didn't just park in the back of the club to begin with. 
Although, another thought is that Stan already knew someone was following him and thus didn't take the direct route to the butterfly. If he parks in front, there would be more traffic, more witnessess, he wouldn't be as isolated as he would be if he parked in the back alley of the club.
Loved the episode. Loved how Castle got Beckett and Ryan as interested as him in the 1940s storyline. Glad they found a way to get Martha and Alexis involved in the episode even if they weren't playing themselves.
The whole "Boyo" exchange was silly fun. And hey we got another Kate and Castle kiss, though not as themselves.
Preview for next week's two parter looks good. The Castle two-parters have been good in the past. Wonder if Castle's past girlfriend and what looks like Castle being put in mortal danger will finally get Beckett to admit her feelings to Castle.
I'm thinking that because wasn't it rumored that the creator, Marlowe, said that the two would be together this season at some point. And by the end of the two-parter, it'll be 2/3 of the way through this season.