My suggestion is for the following feature:
Either:
Add an information panel when users enter the Toll and HOV passes page for the first time, informing them that adding passes may route them into areas or through restricted roads.
Or:
Allow us to add information against each pass/permit, giving the user guidance as to what each pass is for.

My suggestion solves this problem:
There is less chance that the user will select a pass/permit that they shouldn’t have due to the misunderstanding of how the pass system works.

In more words:
Now that Passes/Permits that users have added to their accounts are being passed through to URs in the editor, it’s become obvious that users are adding passes that they shouldn’t be adding. This may be down to a misunderstanding of how the Pass system works. Do the users think they must add the pass to avoid such routes? Maybe.
Adding instructions to the Passes screen or information to each pass individually (preferred) on when to add the pass will give the user a better experience and not be routed where they shouldn’t be but also reduce the amount of URs being raised due to these unexpected routes.