The Potters centre-back was involved in a confrontation with Manchester United striker Robin van Persie in the tunnel at half-time of Saturday's 3-2 defeat, which resulted in him being booked in the dressing room during the interval.
Reports suggested the bad feeling between the two continued after the final whistle and it has been claimed it was related to Shawcross breaking the leg of Aaron Ramsey - Van Persie's former team-mate at Arsenal - in 2010.
Shawcross has also managed to upset other players on the field with midfielder Marouane Fellaini sent off for headbutting the centre-back while playing for Everton last December after the Belgium international snapped following a running battle with his opposite number.
But Hughes insists that does not mean Shawcross should not have a reputation for anything other than being competitive.
"He goes about his business in the way that is most effective for him," said the former United and Chelsea striker.
"He competes and doesn't like getting beat, and they are not bad qualities for a centre-half to have as long as he doesn't over-step the mark.
"People are trying to make a connection between Ryan and Arsenal but it is very tenuous what they are trying to do.
"That was not anything to do with what happened at the weekend. We were playing Manchester United so why would Arsenal come into it?
"It was just a case of a centre-forward and a centre-half going up against each other and they clash now and again.
"Me and Martin Keown used to go at it hammer and tongs - you probably needed two balls, one for us two and one for everyone else.
"There was one incident earlier in his (Shawcross') career which had consequences for another player which is well-documented and I don't particularly want to keep raising it but I don't think it was a consequence of the way he plays.
"Ryan is a good centre-half who is an accomplished player."
Hughes takes his side to Sky Bet Championship side Birmingham on Tuesday for a Capital One Cup tie he hopes will provide some respite from a league campaign which has seen them collect two points from the last six matches.
The competition, in its various guises, holds a special place for the 49-year-old as he scored his first goal against Oxford on his full Manchester United debut in the 1983/84 season.
"It has featured prominently in my playing career," said Hughes, who won the League Cup as a player with United, Chelsea and Blackburn.
"I know some clubs prioritise the league very early on in the season but I think with the squad I've got and their capabilities we can manage a cup run.
"We have come through the disappointment of the United game and we have a game very quickly after that to get over it."
Hughes has a significant personal landmark approaching later this week and does not intend for a cup exit to spoil it.
"It's my 50th birthday on Friday so I want to be smiling as well," he added.