You can find legal cause to challenge practically any decision of a customs authority by an administrative or judicial procedure. You need to be aware that in most cases of court appeals the decision is often made in favour of the participants in the foreign economic activities!
There’s no need to be afraid of challenging decisions, or challenging the lawfulness of actions (or omissions) of customs officers, appealing against the rulings concerning administrative offences by an administrative or judicial procedure. It doesn’t mean that your actions will harm your relations with the customs. Thinking about all pros and cons, please consider the economic effect that an impugned decision of the customs authority will have on your business.
If you are planning to continue participating in the foreign economic activities in future, this step will help you to achieve great economic results and prevent from the harm caused by the efforts of the customs to fill the state treasury at the expense of your company!