I have no idea what that is supposed to mean...
but regardless, you misinterpreted my statement. If it was a reasonable conclusion to the average person with an average mental capacity that you were refunded your ticket by swiping it the second time, your argument becomes extremely weak. Unless there are a lot of people being charged with this crime, it can be suggested that most people understand that what you did caused your fare to be refunded and as such, no longer have a valid ticket to ride. Therefore, if you attempted to ride, it would be a matter of evading the fare.
If this is a big issue to you, if you believe it is worth it; argue your claim in court. If you can convince a court you totally misunderstood what was happening when it stated "$$$$$$ refunded" or whatever the specific verbiage was, you might win. Of course, a judge or magistrate who is more familiar with the system than I might know that your argument is simply ridiculous or it has credence. That is something you will have to consider when making your decision to fight or accept the citation.

