There is a bug with the theme in use in the course. It sets the width of the bounding box to 90% of its natural with. This is a mistake, and is what is causing the bounding box to overlap your equation. Ignore it for now. It is fixed in the release version of the theme, but doesn't seem to be fixed here.
(The slides for my presentation included several features that work behind the scenes to fix some of the problems with the theme, and this was one of them, which is why your version in problem 88 worked properly.)
PREP 2013 Question Authoring - Archived
bounding box surrounding problem in display
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