Here is the scenario as I observed it: (note that these' aren't proper hg branches, just different heads being tracked by bookmarks):

1 - On branch A - commit a modification to ~12 files
2 -on branch A - start modifying 2 files, don't commit because you realize you want these changes on branch B
3 - Shelve the pending files from branch A
4 - Update to branch B
5 - Unshelve the files on Branch B

When I unshelve, I get the modifications to the 2 files that I never committed in step 2, but I also appear to get the modifications that were made on Branch A in the commit from step 1. Those other modifications weren't part of the shelveset and don't belong on Branch B, but seemed to come along for the ride. I'm guessing this is somehow related to the fact that I shelved while branch B was checked out/active.