Over the weekend there were dozens of complaints in the Google forums and other SEO forums about the link tool not showing the right number of links or no links at all. By the time I spotted the issue (Sunday afternoon), the bug was fixed according to Google.
However, today I saw that Google said that although the bug is fixed, the reports will be slow to update.
Googler, Jonathan Simon said in a Google Webmaster Help thread:
Last Friday we had a lag in the link counts being reported for some sites in Webmaster Tools. You may have noticed this issue in the "Links to your site" feature if you saw link counts of zero or link counts that were much lower than what was being reported for your site previously. The good news is that the reporting system for "Links to your site" is once again running normally. We expect it will probably take a day or so before all sites in Webmaster Tools are refreshed with the most recent link counts.
Apologies for any inconveniences this may have caused and thank you for your patience.
I hope by the end of today everyones link reports in Google Webmaster Tools is up to date.
However, there are many SEOs claiming that since the link report bug, their rankings have tanked. Of course, we all know the bugs in reports in Google Webmaster Tools have no impact on Google rankings in the search results.
Forum discussion at Google Webmaster Help.