It's supposed to be amusing, not dark- much like Ana getting bawled out by the landlady who mistakes her for some cheap harlot that Joe picked up on the street, or Joe "borrowing" the camera from the little girl in a later scene at a fountain.
Not really sure it's dark. It seemed to me like she was just confused and wondering why she was in different clothes with a man she'd never met standing over her. It's funny.
There is a more innocent explanation for Ann's reaction in that scene. Remember that early on she expressed her linkings for pajamas, especially wearing only the top part. Then in Joe's bed, she freaks because her first thought was that the bottom part was missing as in "be careful what you wish for".
__________ Last movie watched: Pickup on South Street (7/10)
I just watched this in a packed house at the Coolidge Corner Theater in Brookline, Mass -- I'm guessing they had 300 people for their monthly "Big Screen Classics" series.
This was, I think, the scene that got the most laughter. As others have pointed out, when she realizes she's in pajamas, she suddenly wonders whether she put on the bottoms or not, since she had already expressed a desire to leave them off, and she has to check to make sure. The way Audrey plays this is pure comic gold.
Prepare your minds for a new scale of physical, scientific values, gentlemen.
Yes, but it was also a double entendre. The first thing Joe says after she reaches under the cover is, "Did you lose something?" And she shakes her head, "No".