Hughes was critical of referee Chris Foy after the official took no action over Hammers midfielder Song's rash-looking tackle on Potters forward Mame Biram Diouf in the build-up to the visitors' first goal.
The manager felt it had been a "dangerous" two-footed challenge that potentially warranted a red card, and that Foy "should have stopped the game there and then".
Then asked if he would be taking the matter up with the Professional Game Match Officials Limited, which Riley heads, Hughes said: "We'll ask about it because it's a poor decision.
"We are not trying to get people into trouble, we'd just like observations about that
Our view is that the game should have been stopped."
Regarding a sliding tackle by Southampton's Morgan Schneiderlin on Stoke's Jonathan Walters in the Capital One Cup tie between the two clubs on Wednesday, Hughes added: "That was two-footed again.
"Those type of challenges need to be stopped and something done about it."
Hughes has no doubt that Diouf only emerged from the Song incident unhurt because he jumped out of the way.
And, alluding to the recent controversy over the way Stoke captain Ryan Shawcross marks opponents at set-pieces and accusations that winger Victor Moses is a diving "cheat", the manager said: "I think that (Diouf jumping out of the way) is maybe the honesty of our players.
"We have been criticised and labels have been thrown at a number of players in recent weeks, and maybe people should give us credit for staying on our feet."
Hughes also claims Stoke are not getting as many free-kicks in their home matches as other clubs do.
He said: "We are a little bit anxious.
"More often than not, home teams get more free kicks for them
I think that's fair to say - it's just because you are the home side and that's what happens.
"The crowd's with you, they'll cheer and shout, and more often than not, you can look right through the league, home sides get more free kicks - apart from Stoke City."
Source : PA
Source: PA