Sometimes just hovering over a drawn structure in JChemPaint leads to permanent distortion of the graph.
See attached example screenshots. There is the normal structure, opened from a Chebi Mol file, and the distorted, after just hovering around a bit with a benzene ring. Hard to re-produce the event though.
The error is related to Point2Ds with NaN values, happening for ringPlacer.placeSpiroRing.
Undistorted picture
Voila