The core part has a variety of problems. Alignment is correct, but all pins are defined as female (and thus won’t connect to the breadboard which is the problem, not alignment, male and female in the fzp file do not refer to the sex of the connector but rather whether the pin will connect to breadboard or not) but all that I saw are fixed in this part. There are still more (it doesn’t meet the graphics standard for instance) but everything functional that I saw wrong is fixed.
edit: I have upgraded the part(s) to meet the graphics standards and added the 5V version to the 3.3V version.
Arduino Pro Mini (3.3V)-fixed.fzpz (16.8 KB)
Arduino Pro Mini (5V)-fixed.fzpz (16.8 KB)
Note you may need to set the grid size to 0.05in (View->set grid size) in order to be able to attach to the breadboard. If Fritzing chooses to use the female connectors as the reference the parts won’t attach to the breadboard because they are misaligned (the interior pins are offset 0.05in!)
Peter