This has to do with the way your axes are set up. There is probably some legacy code (pre Matlab 2006) computing the orientation of the arrowhead based on an assumption that your y axis is bottom to top and x axis is left to right (in ascending values).
As I can see from your plot your x axis runs descending from left to right. If you change this it should correct the arrow position. I've only ever experienced this problem with "imagesc" plots myself where the y-axis is inverted and a simple
clears it up for me. Maybe it is different in this case since it does not look like an imagesc axis but I still think the underlying issue is with how the "arrows" annotation (head) does not seem to work correctly when the axes are not standard cartesian orientation.
Hope this helps.