Hi Kirasun,   
Unfortunately, this "bag glitch" is a known glitch, mentioned in the General Support FAQ, quoted here for your convienience: 
    
What this bag glitch created when the game crashed is a situation similar to the data loss during a rollback, which is explained here.  As mentioned in the post, quoted here: 
    
There is no way that we are able to determine whether a masterball, or any object was used during a rollback situation, where the data that was lost is irrecoverable, so unfortunately we are unable to do anything in this situation.   
In order to avoid this situation in the future, I would follow the recommendation of opening your bag every 5-10 minutes; it fixes any lag that you may experience from the bag glitch, and any further loss of data because of it.   
I hope you have a nice day ^^ 
 [glow=green]Locked as resolved[/glow]