David Bentley burst into the box with eight minutes left, Gilberto stood his ground and the pair collided - referee Peter Walton waved appeals away.
Hughes said: "It was a penalty. David has picked up the ball in the midfield area and burst forward with real purpose at the heart of their defence.
"The guy has obviously stood in front of him and actually made a move with his leg to make sure David went down.
"The very minimum it should have been is obstruction, and that wasn't given either. We felt it was a certain penalty.
"We are a little disappointed with that because we had done really well to get back on level terms.
"We didn't start at all brightly, Spurs were better in that early period. If you give good players time and space they will pick you off, which they did.
"I think our goal stirred us, we were better after that. The second half could have gone either way but I always felt we could create opportunities and the penalty would have been a key decision had it gone for us."
Mark Hughes felt his side were denied a late penalty in Saturday's 1-1 draw at Ewood Park.