Morrison has a bruised foot whilst Clarke twisted his ankle during the extra time defeat to Hartlepool United on Wednesday.
"Clinton's got a badly buised foot and he got clumped on it as he tried to have a shot just before the end of normal time, " said Chris Coleman to the CT.
"It hasn't done him any favours in terms of the weekend, so we'll have to wait and see what happens over the next 24 hours.
On Jordan Clarke, Coleman said: "Young Jordan twisted his ankle which hampered him a little bit. He's a tough kid and he carried on but then he cramped up and had to come off."
Keiren Westwood, Sammy Clingan and Aron Gunnarsson were all involved in international football on Wednesday night but are back and included in the squad. New signing Martin Cranie is also in the squad.
Patrick van Aanholt, whom Chelsea did not want cup tied, is expected to play at left back but striker Leon Best is doubtful with a bruised shin.
For Barnsley, Darren Moore has a toe injury and is doubtful.
Former Leicester City striker Iain Hume, who was sent off last season, could feature as could winger Mounir El Haimour and Argentinian Hugo Colace.