Hi Chas,
Maybe this helps you see what is happening. If you have a flight plan, each time you "Direct-to" a future waypoint in your flight plan, it will add or insert your current position as an "actual" reference point. Think of it as creating an actual breadcrumb of the past point you used the direct-to option from the Flight Plan page.
It should not be adding waypoint magically, only if you add a waypoint, direct-to or rubberband the route line. If this is happening, please call us so we can get a bug report.
There are some changes to how the Direct-To function works in the 9.4. You can have a Flight Plan, then Direct To a alternative point, and then revert to previous plan. Version 9.4 should be out in a few weeks. Stay tuned and if you need some additional information or support on this, please fell free to contact our support team. Hope you have a great weekend.