Bar width gets too large

I'm creating a plot with the plotyy function to draw some bars together with a line. The bars are have the same color.

For some bars, I like to change their facecolor. I notice that the facecolor of the bars is not actually changed, but overlayed with a new bar. For some data, this works fine. However, there is one set of data where the width of the overlayed bars is too large. Even if I define the width, it is overruled by Maltab.

Is there somebody who recognized this behavior?