Shea impressed during his first appearance under Hughes, setting up the opener for Michael Kightly before adding the second himself.
But his involvement was ended early by a challenge from Matt Kassel, with the club initially fearing the 23-year-old has suffered damage to the medial ligament in his left knee.
Shea will undergo a scan on the injury, but Hughes is expecting a lengthy lay-off.
The Welshman told Stoke City Player: "He will go for a scan tomorrow, but we know that we will definitely be without him for a number of weeks. It looks fairly serious but fingers crossed it isn't any more serious than we already know it is."
Hughes was also critical of Kassel's challenge.
He said: "I really have no idea what the lad was thinking about going in for the challenge like that.
"Maybe he was trying to make a name for himself - I have no idea. But whatever he was thinking it was totally wrong."
Source: PA
Source: PA