Hi there
Keep in mind, Google WMT only passes along data to Analytics in rounded increments of 5, 10, 100, 1000. You're better off checking your WMT data directly to get more clear, granular numbers.
For instance, one of my clients has a branded term in WMT for March 2015. I checked the same one in GA:
WMT - 15,167 impressions
GA - 15,000 impressions
For another term:
WMT - 1 impression
GA - 5 impressions
If it's not zero, but less than 5, it's 5. This should be why you're seeing this, but you would have to compare your GA and WMT data up against each other.
Here is more information for you if you from Google WMT Help.
Hope this helps! Good luck!