Most likely, what you saw was referring to the free version. We have had, over the last year or two, a few reports of problems with the free version too--enough that a couple of my fellow Gurus will no longer recommend malwarebytes at all--but under most circumstances you should not have any problems running malwarebytes FREE alongside your Norton.
Malwarebytes PRO is, however, another matter. Our experience here suggests that running the two (or any two real-time security programs) together will eventually cause problems--and even in the meantime will leave your system more open to threats. It can also cause other confusion--for example it is most likely having malwarebytes pro installed simultaneously that caused NPE to detect a part of itself as malicious--the problem that originally brought you here. I think most of us would sooner see you uninstall Norton than that you keep running it together with another real-time security program (though that's obviously not what we'd recommend).
What's more, it's not even sufficient to "unactivate" the second real-time software to avoid this issue; you need to uninstall it, using its custom removal tool. This seems to be an industry consensus, and even malwarebytes itself has started recasting its marketing around this concept. Note the presentation, at the download link I provided above, of MBAM as "Because you and your antivirus need a wingman" (emphasis added, suggesting that this is the product they offer for folks who have other primary--i.e., real-time--antivirus protection).
For malwarebytes, their custom removal tool can be downloaded here:
http://downloads.malwarebytes.org/file/mbam_clean
V/R,
--DistEd2