The first difference that I noticed in the conversion to film is the pacing of this storyline. In the book, it takes a while for Clary to understand what the shandowhunters do, what she can do and how she is a part of their world. She also learns about her mother and what she is toward the end of the book, just like the movie, but the time it takes for her to get there is substantially longer. In the movie, everything is very fast-paced and it is hard to see how Clary found everything out about everything that she did in the amount of time the movie gave.
Another change from the book to the movie is the way the first scene is handled with Clary's mother. Jocelyn. In the movie, Jocelyn is shown to be strong and fighting the demons that attack her. In the book, it seems as though Jocelyn did nothing to save herself and Clary is left to fight the creatures that she couldn't. Also, the way Clary kills the creatures is different. In the book, she throws the sensor in its mouth and it dies. In the movie, she sets things on fire and sets off an explosion to get rid of them. Either way, Jace has to come back to help her.
The very end of the movie with the portal was set in different locations. In the movie, it is in the institute, but in the book it is in an abandoned mental hospital on an island that they must drive to in order to save Clary's mother. Luke, Jocelyn's on-and-off boyfriend turns out to be a werewolf and is the one who helps Clary save her mother. He and his pack fend off Valentine's people while Clary goes inside to get her mother. Luke's entire story is different, and a bit sped up from the book.
All in all, a O.K. book-to-movie adaptation. Not the greatest, and then were quite a few important omissions, but I think that if a sequel is made, they can improve on it a lot. Overall, I would give this adaptation a 2.5 out of 5 rating.