For instance, jsdom's more spec-compliant parsing causes issues with auto-closing elements (lifehacker article) and with not having self-closing <img> and <br> tags. The former was fixed by removing offending markup, the latter by adjusting JSDOMParser to be more sane, and the expected outputs to cope with this.
Finally, JSDOMParser automatically drops comments. The test code needed to manually do this in the jsdom case.