We don't have nearly enough information to understand what's causing those results.
Shots in the dark include.
- You're using the BaseValue property of the bar() function to vertically offset the bar plot downward. The solution would be to remove that name-value pair or set its value to 0.
- The y-tick labels have been set such that they no longer correspond to the actual y-ticks. The solution would be to stop setting the YTickLabel property of the axes.
- Those are patch objects whose vertices are correctly mapped into the axes. If the place of the patch is unexpected, the solution would be to correct the patch vertices.