I ran the following query in REST Explorer ( on ApexCodeCoverage ). Im getting duplicate (and wrong) results. Few classes/triggeres are repeated with different results.

    /services/data/v29.0/tooling/query/?q=SELECT+ApexClassOrTrigger.Name,
+ApexClassOrTrigger.Id,+NumLinesCovered,+NumLinesUncovered+FROM+ApexCodeCoverage

As highlighted in Yellow in the below image, the class ApplicationInfoHelper is being repeated many times in the results, with different lines (un)covered results. Same with many other classes in these results.

Atleast the lines covered/uncovered should be same, even if the class is repeating. [Note the Ids are the same, so I'm sure it is the same class]