Forest's top goalscorer was awarded the opening goal on the hour mark as substitute Zach Clough's shot deflected off him when he was standing in an offside position.
It sparked long protests from the Albion players, but after consulting with the linesman referee Oliver Langford allowed the goal which sent the visitors on the way to their second consecutive defeat.
Forest then made the points safe with a minute remaining as David Stockdale miscontolled a back-pass and Ben Osborn netted, before Clough converted an injury-time penalty.
Hughton said: "I wasn't sure what it was at the time, but I have seen it again and he looks offside. Whether the referee knew Assombalonga had touched the ball, but I presume he was made aware of that, but certainly he looks offside and changes the game.
"The fact from what I have seen, he looks like he is in an offside position and the person with the best view of that is the linesman and you would expect him to give that. Now, in the end if he doesn't know Assombalonga has touched the ball I can understand it, if he is aware of that, then he is in an offside position.
"The second and third goals are both, from our point of view, bad goals and probably a little bit of a reflection of our performance overall. I can't say we genuinely deserved to win the game, we needed to test them more when we got into good areas in those last stages. It certainly wasn't through a lack of trying, but we needed to show more of that over 90 minutes.
"It was massively disappointing. We needed to show more energy especially in the first half, but we got through to half-time not at our best. We knew we needed to raise our game and we were able to do that.
"At that stage, they had the first (goal) which made it tougher, we had to change the shape a bit and certainly we have conceded two really poor goals after that."
The Albion boss, however, stood by his decision not to freshen up his side after making just one enforced change with Liam Rosenior making his comeback for the injured Sebastien Pocognoli.
Hughton added: "I am always tempted (to make changes) when I look at the players I have got in the squad, but I think we were doing well enough. We were on the back of three good performance irrespective of one being a defeat to Newcastle.
"I thought the performances were good enough that we could go again, particularly away from home we have been fairly settled the last few games. With regards to the energy levels it certainly wasn't down to that."