The 36-year-old striker netted his 100th Premier League goal with his fourth in five league games to put the Potters ahead after seven minutes, converting from Marko Arnautovic's square pass on Wednesday.
But Ronald Koeman's Everton drew level after 39 minutes when Seamus Coleman's shot deflected off Ryan Shawcross and into the back of the net, though it had first been called offside with the linesman believing an offside Romelu Lukaku got the final touch at the Bet365 Stadium.
Replays showed that the ball actually nicked off Stoke skipper Shawcross but Hughes believes the goal should not have been awarded regardless because Belgian striker Lukaku made a movement towards the ball.
Stoke boss criticises referee, insists he 'should've been a little bit stronger'
He explained in his post-match press conference: "In my view, it's offside. He's in an offside position when the ball is played by his teammate.
"It has obviously hit Ryan on the way through but he's in an offside position and then he's made a movement towards the ball as it goes past.
"My view is that if you make a movement then you're distracting the keeper. You don't have to just be in the eye-line, you've just got to make any kind of movement because for the keeper you have to wait until the ball goes across the player before you can react.
"Clearly, because Lukaku is there, he [Lee Grant] couldn't react any quicker than he did. In my view, it's offside. In fairness to the referee, he got surrounded by a lot of Everton players and really should've been a little bit stronger and made the decision and got on with the game.
"But as it was, he caved in a little bit and went over and consulted. Having heard what the guys have said and been in, I think the linesman actually said he flagged for offside because he thought Lukaku had touched the ball.
"Clearly he didn't but even so I still think he's offside."
Hughes: Crouch has made 'real impact' over his career in the Premier League
Despite the disappointment of drawing having been the better side in the first-half, Stoke move up to ninth with the point which means they are still unbeaten in the league in 2017.
On Crouch's phenomenal achievement, becoming the 26th player to reach the milestone of 100 goals in the top-flight, Hughes continued: "Yes, great story, great moment for everybody who was here to witness it in my view.
"It's a special moment for him and his career and we saw the robot dance coming out to good effect. I think everyone enjoyed that moment. So, really pleased for Peter.
"Have to say since he's come back in the team he's been excellent and I thought he was very good again tonight.
"He took his goal really well, a well-worked goal. Good ball from Marko after a great pass from Charlie [Adam]. At that point I thought we were good value [for the lead].
"We had a couple of other chances that Marko could possibly have taken, but we were much the stronger team in the first-half. And they get a life-line really with the offside decision.
"But going back to Pete, in fairness to him he's been doing that for the whole of his career. If you give him good service and put the balls in the right areas, then he will create chances and take them.
"He's hit milestone that is something special to him and he probably thought that maybe it'd passed him by but he's stuck at it, been professional and waited for his opportunities. Credit to him."
Hughes also joked that Crouch was "a bit rusty" with his iconic robot celebration, which he brought out for the first time since 2006, but added: "It was a great moment and everyone enjoyed seeing him do it.
"As a manager, from my point of view, I was more pleased to see the ball in the back of the net to be perfectly honest but the significance of the moment is huge for Peter.
"He's in a select group of players that have had a real impact at Premier League level and no-one can take that away from him now so credit to him. He's a great guy and a great player as well."
Hughes backs Berahino to improve as striker gets sharper fitness-wise
Another major positive was Saido Berahino making his debut from the bench after joining from West Bromwich Albion less than a fortnight ago.
The £12 million striker looked bright and saw a late attempt cleared from the line by Everton centre-back Ramiro Funes Mori.
On his 25-minute cameo, the Stoke manager said: "That's what he needs. He needs match fitness. He's not there yet, you could see that with some of his play but the quality of his runs was on display.
"He made two or three really good runs that we missed him with a couple, but Charlie picked him out with a great ball and that was due to the quality of the run and I think two or three weeks down the line, that'll be dispatched and that'll be a goal without even thinking about it.
"I think he was a little bit deliberate trying to get his first touch right and thinking a little too much about the opportunity. But it would've been a great story, arguably up there with Crouchy's maybe."