I noticed this because an employer replied to their notification of my application (with me as a recipient). My cover letter included a richtext hyperlink to the job listing page (copy-pasted either from GMail or MS Word). The URI is erroneously relative, like so:
Any link in this format will be broken, when trying to use it, in the email because there's no base URI ("careers.stackoverflow.com"). The cover-letter-editor (pop-up that shows when clicking the apply button) doesn't have the full markdown editor (there's only "B[old]" & "I[talics]"). Maybe, as a workaround, hyperlinks should just be stripped altogether.
I don't understand why the base URI is stripped (maybe for flexibility somewhere[?]) but I saved my cover letter elsewhere and it has the base URI, there. I don't know how to test this any further without sending an actual application and/or creating an employer profile.