Swansea defender Chico Flores deftly flicked home a 52nd-minute equaliser at a windswept Britannia Stadium to cancel out Peter Crouch's 17th-minute opener.
"We got our noses in front and hoped to go on from that, but we never really did. Performance-wise it wasn't one of our better ones," said Hughes.
"On reflection, I'm disappointed given our lack of control in the game, and we've been better than that at the Britannia."
Hughes did feel a couple of penalty decisions went against his side, with Crouch seemingly clipped by Chico and a potential Wilfried Bony handball.
Hughes added: "They were two big decisions that could have gone for us, but it would have been a little unfair on Swansea.
"They had further chances to score, with Asmir (Begovic) making a couple of great saves, and Ryan (Shawcross) clearing one off the line."