That is an inexcusable reason for having this error creep into the film. There are sites, including Memory Alpha and Memory Beta, that contain information on Star Trek technology. And there are things called dictionaries, with some them being available for free access on the net, where words are defined.
Best to stick with what Memory Alpha has to say about it, because from the dictionary definition, technically the engineering hull could be described as a nacelle too.
A separate streamlined enclosure on an aircraft for sheltering the crew or cargo or housing an engine.
[French, dinghy, gondola, from Old French nacele, small boat, from Late Latin nvicella, diminutive of Latin nvis, ship; see nu- in Indo-European roots.]
I remember from the film another interesting tech note. When the shuttles are entering the Vengeance spacedock, the audience hears a public announcement that a welding team was to do work on nacelle 1. Now, is nacelle 1 the starboard or port nacelle? What do you think?
I think it doesn't matter, because from a character perspective they know exactly what is being referenced. From the audience perspective it's just supposed to be a bit of background minutiae to add to the depth of the environment and make it feel like a real place where people are working.
If you went to a factory or an airport in a movie and didn't hear occasional announcements over the PA it would seem weird.