In this paper, acoustic analysis of misarticulated trills in cleft lip and palate speakers is carried out using excitation source based features: strength of excitation and fundamental frequency, derived from zero-frequency filtered signal, and vocal tract system features: first formant frequency (F1) and trill frequency, derived from the linear prediction analysis and autocorrelation approach, respectively. These features are found to be statistically significant while discriminating normal from misarticulated trills. Using acoustic features, dynamic time warping based trill misarticulation detection system is demonstrated. The performance of the proposed system in terms of the F1-score is 73.44%, whereas that for conventional Mel-frequency cepstral coefficients is 66.11%.