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I had same problem and when I change type of dictionary float to unsigned char it works.

cv::Mat floatdictonary; // floatDictionary = bowTrainer.cluster(floatFeaturesUnclustered);//you have convert features //unsigned char to float cv::Mat udictionary; floatdictionary.convertTo(udictonary,CV_8UC1); // bowDE->setVocabulary(udictonary); Mat bowDescriptor; std::vector<std::vector<int> > pointIdxOfClusters; bowDE.compute(img, keypoints, bowDescriptor,&pointIdxOfClusters);