The classical $k$-means clustering requires a complete data matrix without missing entries. As a natural extension of the $k$-means clustering for missing data, the $k$-POD clustering has been proposed, which ignores the missing entries in the $k$-means clustering. This paper shows the inconsistency of the $k$-POD clustering even under the missing completely at random mechanism. More specifically, the expected loss of the $k$-POD clustering can be represented as the weighted sum of the expected $k$-means losses with parts of variables. Thus, the $k$-POD clustering converges to the different clustering from the $k$-means clustering as the sample size goes to infinity. This result indicates that although the $k$-means clustering works well, the $k$-POD clustering may fail to capture the hidden cluster structure. On the other hand, for high-dimensional data, the $k$-POD clustering could be a suitable choice when the missing rate in each variable is low.