Starting from R2014b the entire graphics engine was reimplemented. While R2014b graphics makes most of the graphics better it also has some issues, for example, extracting images with circular shaped markers in EPS or PDF file format.
The development team is already aware of this issue and they are considering fixing this for a future release of MATLAB. Unfortunately, at the present moment there is no workaround for this.
The two possible things that the user can do is:
1. Use a different marker shape in MATLAB releases R2014b onwards; or
2. Use prior releases than R2014b.