Okay, having seen this same issue hit us on 5/7 I've been digging around for potential causes.
Background: 10+ year old website, e-commerce, unique industry and Amazon and Ebay do not participate in. Hit bad with Panda 1, have been increasing in ranking, traffic, impressions, and conversions since we started working on addresses Panda issues.
The only thing we've done really in the past year is continuously add new products to our website. Running Magento Enterprise, and we use original content that is well written and consistent after the initial Panda.
What I've found so far:
1) We have some issue where Magento's URL rewrite process has went crazy with specific products. It appears to be ones that shared URL keys, where Magento made the next one be widget-type-####.html whereas the first one was just widget-type.html. I've found on average 200+ url's that were created on each product. Rel=canonical is turned on, yet each of these mistake created products through the URL rewrite process has it's own rel=canonical for its URL.
2) We had around 120~ internally linked pages that were returning 404s.
We've addressed #2 and we're working on cleaning up #1.
The interesting thing is, some how Google has found around 54 of the URL's that were generated incorrectly through the Magento URL rewrite process. I do not see them in sitemap we submit, and Screaming Frog did not find any in the scan I did. So it is a big mystery as to how Google found these URL's, why they only found 54 out of the thousands.
I hope that helps someone. Basically my advice would be keep looking, there is most likely a situation like we had, where a problem you wouldn't normally see has been found by Google and it is hurting your rankings.