Pompey managed to keep Pools at arm's length as they are they only team below them in the table and would have overtaken them with victory.
Hughes, whose side are four games unbeaten but still bottom, said: "It's frustrating. Expectations were on and winning would have put us off the bottom.
"We were missing that wee bit of magic to open up the defence, that killer pass.
"On the other side it's unbeaten in four and a clean sheet. But I'm disappointed as this was there for us to move off the bottom - a good chance at home.
"We tried to stretch it, changed formation, used substitutes, and it didn't happen. We had half-chances, but couldn't get through."
Hughes had billed the game as a "cup final" for his side, who lacked a cutting edge.
He added: "They are no mugs, they have a lot of experience. All credit to them in terms of the situation they are in. They were spirited but it was up to us to produce something to unlock the door and make them open up.
"Sometimes you get frustrated but you take it on the chin and go again."