I recently came across an issue where SharePoint was not indexing some Site Collections and the crawl logs were showing the following with reference to the problematic Site Collection:
"The SharePoint item being crawled returned an error when attempting to download the item"
It turns out the start page of the root site contained a search result webpart which was causing the crawler to abort the rest of the crawl.
This issue has since been fixed in a hotfix. Install the latest CU to solve the issue.