There has been a bug in Google Webmaster Tools lingering since July of this year where missing data is not found in the "Download all sources of errors on this site" report.
Michael Martinez wrote a new Google Webmaster Help thread summarizing all the complaints and issues with the download. He linked to several threads with the issue and saying there has been no response from Google.
Well, that got Google's attention and they replied.
Jonathan Simon from Google said:
First of all thanks for the extra detail you've provided. This is an issue that we're aware of and we're working on restoring the "Download all sources of errors on this site" functionality so that the .csv file it produces includes all the available "Linked From" sources as it did previously.
The issue is on the Crawl Errors report when you click the last download option:
Anyway, there is still no ETA for a fix but it is on Google's radar.
Forum discussion at Google Webmaster Help.