I'm sorry you're going through this very stressful situation. The only thing that I can see being a problem is if the bottle the parent gave you was not exactly as is stated in number 2 of the policy shown.
Our policy in my district and throughout the city for school nurses is that no medication can be accepted unless it's in the pharmacy bottle it came in, pharmacy driven label, name, dose, med, time, expiration date, physician, etc. Anything less goes back home with the parent and I'd notify the supervisor.
So, not to be discouraging, it's not that. But I want to mention that crucial number 2 listed in the policy that's posted in this thread. If the bottle didn't measure up to policy then that's going to be the issue. If the bottle does measure up to policy, then they're wrong.
I hope it will eventually be resolved in a good way for you and that you'll move forward in the best way. Things do go wrong at work sometimes, and usually, hopefully!!, there's understanding about what happened.