My laser (30W) cuts the plexi crystal clear. The protective film when removed, takes any char marks with it, though its usually soot and can be wiped off... if not a quick buff will remove it... whenever my tape measure lies and the plexi finished up a tad bigger, a quick sand/scrape/rasp will fix it before a buff... if I succeed in cutting it too short, I usually have little alternative to re-cutting a new piece... preferably after I change dimensions... may seem a moot statement, but I've re-cut it many times before saving the changes.
If your first cut is too short... Take the second cut from the longer end... LBD