[plugin: Yoast WordPress SEO] Duplicate Meta Descriptions – Sitemap? Help

This might be a duplicate post, so I apologize in advance but I have been searching for over an hour now!

So about a week or two ago, I switched from using the XML Sitemap Generator to using the Yoast Sitemap Generator and resubmitted the new sitemap to Google. I noticed that before switching, the XML Sitemap Generator’s sitemap had around 30 to 40 pages to index. When I switched to Yoast, it had around 250 pages to index.

My positioning and traffic spiked and then dropped like a rock a few days ago. By about 80%. I looked at webmaster tools and now I have over 100 duplicate meta descriptions and 50 duplicate titles!! Before, with XML Sitemap Generator’s sitemap, I had around 3 or 4 duplicate meta descriptions. I know that it’s because of canonical urls and my category organization.

I switched BACK to XML Sitemat Generator’s sitemap plugin and made sure that the categories were NOT included in my sitemap. Now I’m back down to about 50 pages (i added some). I did this yesterday and I’m still not seeing the duplicates drop yet, however, my error pages have.

My question:
Will the sitemap that excludes categories fix the duplicate meta descriptions and titles? Please respond!!