Long stitches is definitely the issue.
Look at your screenshot to the left of the stop point cross hair. Notice that that row of stitches is visually different then the others? That's how long stitches is generated visually in Wilcom.
Also just so I'm uderstanding the "long stitches" issue...is it caused by long runs in the same angle? If I tilt the stitch angle from horizontal (0 degrees) to 15-30 degrees and perhaps move the stop point up to say roughly 75% up the circle would that be a reasonable suggestion to help fix it?
This is me speculating, but it has to do with the stitch engine and how the math handles that last stretch (or row) of stitches. I've seen this is other programs (typically long stitches like this very well with this particular object, are what make seasoned digitizers think auto conversion, this type of stuff always needs to be cleaned up).
What I would suggest doing, is keep in mind what angle that you want it to be (sometimes this is determined by the substrate (as mentioned before) or by the design itself (as you start doing blends etc, angles are going to be more resolute in what they should be)) and try to put the end point is the most out of the way spot to mitigate how this row shows up. If doing a horizontal angle fill on a circle, I would would want my end point to be either the very top or the very bottom. If there is another object that I want that end point to connect to in order not to have a trim, then that may have a bearing on where I put it.
If I'm going to have a 90 degree angle, my end point will either be far left or right. This does get more complicated depending on how complicated the shape is (for instance, if doing a fill stitch of "P") you won't be able to visually hide long stitches at all only try to relegate it to the smallest portion that you can on the object.