The trio have refused one-year contracts and did not return for the start of pre-season training on Friday.
He said: "We would have liked them to stay but I understand their position fully. We have started back to work. I think we have moved on now."
Stubbs has been linked with Wolves and Aston Villa, while Watson is a target for West Bromwich Albion.
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MMIX
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Match of the Day - Post-match interviews