I think your configuring wrong the input structure. Each input vector must be a column and not a row. Quote from this "Clustering Data - MATLAB & Simulink"
To define a clustering problem, simply arrange Q input vectors to be clustered as columns in an input matrix (see "Data Structures" for a detailed description of data formatting for static and time series data). For instance, you might want to cluster this set of 10 two-element vectors:
inputs = [7 0 6 2 6 5 6 1 0 1; 6 2 5 0 7 5 5 1 2 2]
As you can see each input vector is a column. You have 10 two element input vectors as a 2x10 array.