What framing errors would "Alien 3" have? Since it was filmed anamorphically it would seem very unlikely that the transfer would have any errors. Unless it is the bio readouts at the beginning that appear cut off on most displays, but that is just common television overscan.
Chasing Amy has a documented framing error, never corrected (although not a huge deal, one scene, obviously a mistake in prints as well, so the DVD is as it was in theaters- whether ugly or not).
Clerks I had not heard of previously- although given it was shot 4:3 and cropped like 2 years later for theatrical distribution (blown up from 16mm)- there could be a fair amount of debate as to proper framing (adding to which, Kevin has a bit of a "who gives a shit" attitude toward such things). Clerks will be reissued this year sometime- so maybe a new transfer will cure whatever people think is wrong.
Reservoir dogs has so many problems, it's better just to think of it as "unreleased"-- the current SE has incorrect color, horribly blown out image, misframings, missing dialog and sound, and the extras are so cheesy it's cringeworthy!
All of these have been discussed at length here- and a search would find the previous discussions.
You're wrong re: ALIEN 3, it was indeed shot in anamorphic Panavision. It's the only time Fincher has shot anamorphic, all his later films were Super-35.
As for CLERKS, while it was shot in "full-frame" 16mm, the framing was composed during shooting for eventual blow-up to 1.85:1 35mm (incidentally, it was blown up to 35mm less than 6 months after it's first festival screening, not 2 years later). I know for a fact that the upcoming "10th Anniversary" DVD will be anamorphic widescreen from a new High-Definition transfer taken from the 16mm interpositive (the old transfer was taken from a 35mm blow-up source), and was approved by both DP David Klien and Kevin Smith. They were given the choice of releasing a full-frame version and flatly refused. The full-frame version has lots of headroom and neither Kevin nor Dave wants it to be released that way on DVD or in any future HD format.