But the Hibs manager thinks the solution to those problems cannot just come from within the relevant departments of the team. As the clich has it, defence starts at the front, and for Hughes that means a striker such as Anthony Stokes learning how to do more to help his team-mates.
The Easter Road club's top scorer with 20 goals so far this season, Stokes has been at his predatory best from time to time. But Hughes thinks that while goalscoring comes naturally to the 21-year-old, there are other aspects of the game which he will have to work on assiduously before he can begin to realise his all-round potential.
"We will go and train and he'll play in certain areas of the pitch and come off having scored four or five goals," Hughes said yesterday. "But you are saying to him he needs to work back in, because I know he can do it. I am trying to educate him.
"I have no doubt next year I will go and play him in midfield in bounce games so he can get a better understanding of the game, because I think it will make him a better player. But it's grasping the concept of what is required. I want him to become a better all-round player without taking his goalscoring instinct away from him.
"You have to be guarded, because he came on the pitch the other night and scored a great goal. But in terms of dropping in and linking up and slotting people in, he has certainly got it in his locker and I want to see more of it."
Stokes was omitted from the starting line-up in Wednesday night's defeat by Dundee United after feeling poorly because of a throat infection. There was already a strong case for dropping the striker even if he had been fully fit, however, as in some recent games he did not contribute nearly enough to the team.
If his attitude in training is anything to go by, however, Stokes is likely to be back in the Hibs team for tomorrow's lunchtime kick-off at home to Celtic. "He has to train the way he has done over the last two days," Hughes replied when asked what Stokes needed to do to get his place back. He's been magnificent. That's the Stokesy I know.
"He had been on antibiotics for a throat infection and he came in on Monday and trained and he was lifeless. We got him home, but when he came in on Tuesday he would have been better not being there. That gave us a chance to pick another team and make us more solid.
"But when I get the time I will sit him down and show him the analysis and just try and educate him. And that doesn't just go for him – it's everybody."
Indeed, if Stokes were the only Hibs player whose game was lacking in certain respects his team would be top of the table by now instead of aiming to get back on terms with third-placed Dundee United. Hughes has stood by his players in public, commending them for the effort they have shown, but he is now of the settled opinion that he needs to bring in fresh blood over the summer as well as demanding more out of his existing squad.
The inadequate physicality in midfield, for example, could be countered by selecting Sol Bamba in a holding role, but the manager is convinced that moving the big Parisian out of the back four would do more harm than good. Similarly, the lack of verve in the middle might be addressed by giving Danny Galbraith a starting place, but Hughes thinks the teenager is not yet ready.
Instead, he will persevere with what he has for the time being, waiting as patiently as he can for the transfer window to open again in the summer. "I know what I have got here and I know the work that needs done," he said.
"One, we need a bigger physical presence in the team. Two, I need one or two who know the game and who are going to coach and organise. And three, I'm hoping we can instil in the players who are already at this club what is expected of them. And that is success.
"There is a lot of work to be done, but the response I have had from them so far has been really good. We're still battling away to try and get that third spot, and you don't know what might happen. Hopefully we can still do it."