http://libreplanet.org/wiki/List_of_software_that_does_not_respect_the_Free_System_Distribution_Guidelines#firefox
Yes, the problem is that it recommends non-free extensions so thus it can't be included in a free software distro without being modified to only recommend free extensions. Firefox itself is free software so using it is not a problem. You (the user) just has to be careful to not install non-free software.
