Magnitude and phase outputs of bode are 3-D arrays, for representing multi-input multi-output systems. The first two dimensions correspond to the number of inputs and outputs, the third dimension corresponds to the number of frequency points. In your case you have a single-input single-output system, so size(mag) is 1 1 n, where n is the number of frequency points.
To get a standard bode plot you can just do
bode(sys)
If you want access to mag and phase as regular vectors, just do
mag=squeeze(mag)
Arkadiy
