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 ^^
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