Thanks - I just came across the following post related to the same question:

https://groups.google.com/d/msg/adwords-api/V5ZjQaPJl80/BVIqOJZPgLQJ

I think that explains the results you're seeing (which I just confirmed 
also match the results in the AdWords UI).

Cheers,
Josh, AdWords API Team

On Wednesday, May 14, 2014 2:43:34 PM UTC-4, AdWordsApiUser wrote:
>
> Just did. Thanks for your quick reply :-)
>
> On Wednesday, May 14, 2014 11:21:18 PM UTC+5:30, Josh Radcliff (AdWords 
> API Team) wrote:
>>
>> Hi MG,
>>
>> Could you send the following *only to me* by clicking *Reply to Author*?
>>
>>    - Customer ID for the reporting request
>>    - The exact report requests you sent (you indicated that you ran this 
>>    report at least twice: once with *Impressions = 0* and once without 
>>    it)
>>    - Any report output you captured, especially any before and after 
>>    output that shows there was a change in behavior
>>
>> Thanks,
>> Josh, AdWords API Team
>>
>> On Wednesday, May 14, 2014 1:19:15 PM UTC-4, AdWordsApiUser wrote:
>>>
>>> I found today that the query:
>>>
>>> SELECT Query, KeywordId, AdGroupId, CampaignId, Impressions, Clicks, Ctr 
>>>  FROM SEARCH_QUERY_PERFORMANCE_REPORT WHERE MatchTypeWithVariant IN 
>>> [PHRASE, EXPANDED, BROAD_SESSION, BROAD, AUTO]  AND Impressions = 0 AND 
>>> Clicks >0 DURING LAST_30_DAYS
>>>
>>> is returning rows. The Ctr is set to 0.00. We found this as our 
>>> condition was set to "Clicks > 0" only, and while calculating Ctr, we got a 
>>> divide by 0 error and internal debugging revealed this.
>>>
>>> Could someone from the API team comment on this? I believe that this is 
>>> a recent regression.
>>>
>>> Thanks!
>>> MG
>>>
>>

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