Receiving a message in Google Webmaster Tools that reads "Googlebot found an extremely high number" is not uncommon for large sites. We covered it many times, including back in 2008 but the big question is how do you avoid it?
It is not a simple answer. Often there is not much one can do outside of trying to restructure their navigation and site architecture. But John Mueller from Google did post some advice in a Google Webmaster Help thread this morning. He suggested using the nofollow attribute on some links for this specific example. Let me quote JohnMu:
Do you consider this message in Google to be serious and take action to minimize the message or do you ignore it?
Forum discussion at Google Webmaster Help.