A related problem you may be experiencing is that a lot of automated
email, and a lot of mailing list authoring software (used by lists
you may subscribe to) generate faulty multipart emails. Often, they
automatically create a plain text version from the HTML content that
the sender created, but fail to include inline URLs. For example,
if the sender of the message wrote some text with a link, it may be
translated to "<a href="url here">some text</a>" in the html version
of the message, and just as "some text" in the plain text version.
So, if you have mutt configured to show you the plain text version
of multipart messages, the URLs may not be in there at all. If you
use mutt's "v" comment from the index, you can look at the text/plain
and text/html versions of the email and see if that's the problem.
-- Cos