To give an example, letís say your site has lots of impressions for [hotels] and [hotels in santa cruz]. Now, because Instant is quickly fetching results as the user types, the user could see your site in the search results for [hotels] after typing only the partial query [hote]. If a user types the partial query [hote] and then clicks on any result on the page for [hotels], that counts as an impression for your site. That impression will appear in Webmaster Tools for the query [hotels]. The term 'hotels' would also be included in the HTTP referrer when the user clicks through to visit your website.
Itís likely that your site will still see impressions for queries like [hotels in santa cruz], but because Instant is helping the user find results faster, your site may see an increase in impressions for shorter terms as well.