Preview freezes on clicking inside (very small) PDF files
Though I never figured out what caused the problem here, and none of the proposed fixes worked, I was able to avoid the problem by switching to Skim, which is generally less buggy than Preview.

The problem likely has something to do with LaTeX, since all the affected files were built with it. Unfortunately, the problem described here is now moot, because a new bug causes both Preview and Skim to freeze whenever almost any document made with LaTeX is opened.