1. Those lines are actually in your drawing. (Eggbot sees all lines, whether or not you do.)  To find out, select all in your drawing (Edit menu > Select all in all layers), and then in your Fill and Stroke panel (Object menu > Fill and stroke), set the stroke paint to “flat color”, and in the stroke style tab, select a consistent width (say, 4 px).

2. Your pen is raising too slow, or you are lowering it too fast. Play with the delays in the timings tab, if this is the case.

Also, it’s not in any official release yet, (and I mention this because you’ve already done a manual install…) but if you download the latest version of the EggBot source code (“Download ZIP” on this page: https://github.com/evil-mad/EggBot ), the new version has a much-improved hatch fill extension.