Civil rights claims against government agencies generally need to be filed within 6 months of the incident, and keep in mind that officers have quite a bit of discretion in making an arrest. The owner of the store probably convinced the officers that you had stolen property belonging to the store in his presence, and that the officers believed the owner (especially if you were not there to offer your side of the story at the time such statements were made) and the officers based their arresting authority on his authority to arrest (see, e.g., People v. Sjosten (1968) 262 Cal.App.2nd 539 - private citizens may delegate their arresting authority to police officers - check out this Citizens' Arrest guide, too (http://le.alcoda.org/publications/files/CITIZENSARREST.pdf)). If the DA brought charges against you and you prevailed (no plea bargain, conviction, etc.), that could change your options a bit, but more facts would be needed to do a full analysis in that regard, and it is likely too late to do anything about it. Also keep in mind that if the owner came to possess your magazines through this process, you could go after him for the tort of conversion (SOL of 3 years), although your damages wouldn't be very much. Good luck! : )
You may need to provide some more information about your case. From what you've written, it shows the incident occurred 1.5 years ago. Did you file a claim against the department within 6 months of the arrest? Did you ever plead guilty to the charges or were you given a negotiated deal with the District Attorney's office? Was the case dismissed? You may want to consult a police misconduct practitioner to discuss your issues since the first half-year after your arrest is critical.