JR Rail Pass, Tottotori Stn, Koge Stn, Kyoto Stn, Green Car

Hi

Just returned from Tottori, and on the way back I was charged an additional fee. Note it was 'on the spot'
cost about 1800 yen (luckily I had it on me).

The trip was
Kyoto to Tottori Station
Koge Station to Kyoto

My question is why the charge? I went to the JR ticket office after and could not get an explanation.
I received tickets to go from Kyoto to Tottori and I was not charged.
But I noted (after stepping on the train) I was in 1) a "green car" and 2) I was charged at that time.

How can I find out if this was an error? I received my tickets from the JR Ticket office, clearly showing my JR Pass
Is it possible there was another route not told that would NOT have been an additional charge?

Note all the stations have "JR" on them. And the train used was the Super Hakuto type train
And this is one source about the JR Super Hakuto http://en.wikipedia.org/wiki/Super_Hakuto
This just (From the City) only tells how long the travel is : http://www.city.tottori.lg.jp/top/multilang/English/general/access_en.html
I found an "old " post (from about 5 years ago) about a "supplement" and "non-JR track", but that was not mentioned
when the ticket was purchased.

So I guess my basic questions are:
1) Does one have to pay the fee (no matter what car one is one is on?) and
2) Is there a "Non-pay" fee way if one is JR ticket holder.

I can see how that this additional fee towards Tottori can really add up in costs for a group, especially if one is charged both ways, I can see it factoring in a decision on which places to visit, based on JR rail pass..

So if one can help sort that out, it would be great