Bony struck twice after coming off the bench.
Clark said: "Bony is in very good form at the highest level, I watched him over the last few games and he looked very, very in-form.
"You know you have that to contend with if you get in front. It is a huge game for them on Tuesday and we are disappointed.
"His first goal was very good but the second goal we could have done more to prevent.
"You always need that second goal against a Premier League team especially with their fire power, we had chances, but we weren't able to take them."
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