The Briton qualified third and, although he dropped behind the Porsche of Pascal Wehrlein as the German manufacturer showed great pace in Mexico, he battled with polesitter Lucas di Grassi to try to secure a podium.
In that battle, Hughes was also attempting to keep fourth away from the chasing Andre Lotterer, but a yellow flag produced for team-mate Rene Rast - who had pulled over on the exit of Turn 7 after a clash with Oliver Rowland - later came to bite.
Race control rescinded the yellow flag having felt Rast's stranded McLaren was out of the line of fire, but Hughes had not been informed of this and lifted on the run to Turn 9.
This allowed Lotterer to pounce, thus providing an opportunity to deprive the Birmingham-born racer of fourth - which he duly did so.
"There was confusion with what the FIA had messaged to the team, and then relayed to me, in terms of a yellow flag going into Turn 9 on the last few laps," Hughes told Autosport.
"But apparently it was supposedly removed and I didn't get told and there was still a light on at the exit of Turn 6.
"So I lifted and unfortunately Andre got told the road message, so he got me on the last lap."
Hughes explained his difficulties to pass di Grassi, as the Mahindra driver put in a sterling defensive performance to claim a podium in his first race for the Indian team.
Although feeling that McLaren's energy management had been strong throughout, Hughes said that the car set-up was not quite enough for him to make the move on the Brazilian - which ultimately resulted in him overconsuming energy in the latter stages.
"I think in general, P4 was probably where, where we were, if not P3 on a different track. We had good efficiency, maybe not compared to the Porsche cars, but definitely compared to di Grassi we were saving quite well.
"We had an energy advantage definitely at some point, but we didn't quite have the car balance though, so we were struggling a lot with rear grip.
"It meant that, even though I had the energy advantage, I couldn't make a move on him and effectively trying to make that move, I just overspent all my energy."
