What are you trying to clear? Interface counters? QoS counters? I've never seen this, so I would assume it's an IOS bug unless you're trying to clear something that's not cleared by the clear counters command.
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John has asked a very good question. What counters are you trying to clear? It would help us to understand the issue and possibly offer suggestions if you would post the details of what you are trying to do. So post the output of the show command that has the counters displayed. Then post the a screenshot of the command you are entering and any resulting output. Then post the output of the show command that has the counters displayed.