Who cares if 'Mortal Instruments' started out as 'Harry Potter' fan fiction?
In addition to the criticisms of the acting, special effects and storytelling (some say it's packed in to much plot or that it looks like just a setup for the second film -- which probably won't be filmed now), some are criticizing it because it allegedly began as fan fiction based on J.K. Rowling's Harry Potter series. (See here for the latest rant.)
I haven't read any of Clare's series -- which has expanded its universe with a steampunk-y concurrent prequel series -- but the books are popular and the plot details seem to me to be sufficiently different for everybody, including J.K. Rowling's lawyers, to chill-lax. The books and/or the film may be great, or may suck, but I doubt they approach the realm of copyright infringement or ripoff.
The books do sound derivative, but here's a big surprise for at least some of these critics: Harry Potter is derivative. (When I read the first book -- annoyingly retitled from Harry Potter and the Philosopher's Stone to Harry Potter and the Sorcerer's Stone for U.S. consumption -- I thought it was OK, but hardly original, and I declined to read any of the further books in the series until the movies came out and persuaded me to take a second look.) As the above link acknowledges, even Shakespeare was derivative. Hell, I'm confident that The Iliad and The Odyssey were derivative. What matters isn't what inspired a story but what the writer did with it.
As far as the film is concerned, it also matters what the filmmaker and screenwriter did with the book. Maybe they have put some more Harry Potter into the story, wittingly or unwittingly. I'd still prefer to judge the film based on its own merits, not on some perceived connection to another book/film series. Sometimes a ripoff is better than its source (see Norman Jewison's Rollerball and Paul Bartel's Death Race 2000).
I suspect some of these critics/bloggers latch onto this to show their smarts ("Hey, I know this was based on Harry Potter fan fiction! I'm so smart!") or laziness ("It stinks because it's based on Harry Potter fan fiction. Did you know 50 Shades of Grey was based on Twilight fan fiction? Fan fiction sucks.")
Unless you actually worship J.K. Rowling and consider it blasphemy to write anything similar to the Harry Potter books, you can confine your criticism to "I didn't like it because it stunk," not "I didn't like it because it ripped off Harry Potter."