There are several webmasters reporting that their search query report, which now shows impressions and click throughs, is showing a major drop in those impressions and click throughs as of June 2nd and 3rd. The reports come via Google Webmaster Help forums.
Yesterday, one webmaster came in and said:
WT Search Queries number of impressions and number of clicks dropped severely on 6/2 and this drop is not reflected in any other stats including Google Organic visits per Google Analytics.
Several other webmasters came in after confirming they are seeing the same thing.
Google has not confirmed or denied anything as of yet.
Here is a picture of a site affected by this Webmaster Tools bug named SEO Home blog:
You see that drop off? This webmaster said this has zero correlation with Google Analytics, so it must be a bug.
Forum discussion at Google Webmaster Help.
Update: Google has now confirmed this bug.