My issue is similar, except Google is reporting 404 errors on its own JS tracking code! This bug appears not to be isolated to Google tracking code, as GWT is also reporting 404s for 3rd party scripts on our page that use the _trackPageview call.
I did some digging and found the following excerpt from Do 404's hurt my site? on the Webmaster Central Blog:
"If you see 404s reported in Webmaster Tools for URLs that don’t exist on your site, you can safely ignore them. We don’t know which URLs are important to you vs. which are supposed to 404, so we show you all the 404s we found on your site and let you decide which, if any, require your attention."
Based upon the above info, my plan is to follow suit and mark the 404s as fixed.
By the way ... did your 404s return?