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You have the lower case "e" window open (or any letter, really), with all guides, hints, colors off; in essence you have just the outline of the letter and that's it.
However, in the very spot where the bottom left node on the inner contour would be, a very slight line appears heading in a downward direction ... almost as if you have a curve point there instead of a corner and the program is reading a slight extension of the southward point. However, you know after checking that indeed it is a corner point.
So on a whim you click the point at the top of the arc, move the left handle in two spaces (reducing its setting), and that tiny southward-pointing line goes away.
This happens all the time in various forms. The question is, have you improved the overall look of the letter by clicking that left handle in two spaces and removing the line, or is that just a little quirk of the program? I ask because if it does help, I need to go check all my letters for this minor anomoly.