A picture might help understand your issue.
Some ideas that come to mind:
1.debur it and it a let it go.
2.drill it through and put a screw or rivet in it.
3. do some artwork and make it look like a bullet hole or a bug
4. put a decal over it
I ended up with a defect in the rear center of my slider and ended up molding a fairing for the center track cover instead of using the aluminum one provided. It extended over the plexi where my issue was.
I don't know of a filler or process that will fix your defect, but maybe a plexiglass expert will chime in.