A Google Webmaster Help thread has confirmation from Googler, Jonathan Simon, that the page not found errors found in Google Webmaster Tools won't necessarily hurt your Google rankings.
Jonathan basically explained that if someone is linking to a page that is not found, there is not much you can do to prevent that from happening. Jonathan said:
Since you can't control who links to your site these Not Found errors won't negatively impact your site's ability to rank in the search results. It sounds like you've got a reasonable workaround with the .htaccess redirect you mentioned. I'd just keep an eye on the Not Found errors in Webmaster Tools and add redirects when it's necessary.
But it is important to track not found errors in both Google Webmaster Tools and Google Analytics to make sure to redirect the page when applicable, so that traffic is not lost. And it is almost always a good idea to make sure you have a useful and pretty custom 404 page for those reasons.
But ultimately, Jonathan said Google won't penalize you for 404s.
Forum discussion at Google Webmaster Help.