Sorry to hear that, something is not right there in my view. Putting them on the spot and asking for the valve clearance figures whist not giving them time to fabricate some may help focus them somewhat, even better ask for the old shims if they state some have been changed.
I was in the same situation and felt that they were charging for work not done, two hours all in.
Offered to pay for the the work less the charges for valve clearances at which they refused to return the bike. I politely pointed out that the allocated time as per Honda schedule had not been spent on the bike and this could be considered as fraud, if they wanted to get sniffy about it, I could easily take it legal and very public and to the biker cafe just outside.
I left it with them and returned the next day to watch the technician like a hawk doing the job, even took sandwiches and a flask plus a camping chair to make myself comfortable while doing so, but did not need to go to those lengths, they got the picture. Needless to say they are not keen to have my custom in the future, which suits me fine.
Good luck if you decide to challenge it.