You might want to try deleting the two "connector points" on the circle, then you should be able to create a center point using your geometry tools.
You might also want to try increasing the tolerance to a large value when you are extracting your Geometry. This will this will round off small line segments and blend them together. The larger the tolerance, more likely it will extract a circle with only two "Connector points".
If you only want the holes only, you may want to use the Hole extraction function found next to the Geometry Extraction function on the geometry Pallet, again, you may want to increase the tolerance for this tool to.
Hope this helps