Moses, who is on loan at the Britannia Stadium from Chelsea until the end of the season, appeared to have overcome muscle tightness to take his place in Saturday's XI to face Sunderland.
The 23-year-old forward returned to training after receiving the all-clear from a scan, but left the action after just 18 minutes at the Stadium of Light before Stoke went down to a 3-1 loss.
Hughes said: "Victor had a little bit of tightness after the Newcastle game.
"Nothing showed on the scan so he trained on Thursday and Friday and said he was good to go.
"Obviously, almost immediately he felt discomfort and we weren't going to take any risks with him so we made the change.
"We're hopeful it's not too serious.
"Given nothing showed up on the scan, we've got to get to the bottom of it and see what's causing the pain that he's obviously feeling.
"You don't come off in a Premier League game so early unless there's a problem."
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