Hughes's intention was always to give England Under-21 international Jack Butland a couple of games towards the end of the season and last weekend's defeat at Swansea was the first of those.
However, Begovic's decision to tell the Potters boss he did not want to be a substitute at the Liberty Stadium has only increased speculation about his future at the club.
Hughes insists, however, he is not laying the groundwork for Begovic's departure in the summer, although he admits he cannot say for certain whether the goalkeeper will be at the club next season.
"I have said before it was my intention, if I felt it was appropriate, to give Jack some games and that was what I did," said the Stoke boss.
"I told Asmir and a number of other players who were not involved in the starting XI.
"He wasn't involved because he felt he should have been and his mind was not focused to be on the bench - which I understood to be honest and I was okay with that.
"People have misinterpreted this and it needs clarification.
"Nothing has changed from our point of view
I have given a promising young keeper, who we think highly of, a game and he'll get another game and that's it, it is part of his development.
"Whether or not that has changed other people's view of the situation I don't know, but from our point of view it's as we were.
"Our intention is that Asmir stays
We don't know if that is going to be the case at the moment because those talks were always scheduled for the end of the season.
"If Asmir stays we will continue to look to develop Jack and the likelihood is he would probably go out on loan again (he spent time with Sky Bet Championship side Derby earlier in the campaign), if the right club was available."
Butland will start again in Saturday's visit of Tottenham, after which time Hughes will make a decision as to who plays in the final two games.
"My intention was to give him an away game and a home game so he is going to play on Saturday," he added.
"Asmir will not be available because he's just had a slight procedure that he has taken advantage of because he knew he wasn't playing this weekend so he will be back fit and well next weekend.
"Then I'll take a view on the last two games."
While the debate continues over whether Begovic will stay, Hughes, a former Wales manager, had some words of advice for his countryman Gareth Bale.
The 25-year-old has endured a difficult second season with Real Madrid and was heavily criticised after their 2-1 defeat to Juventus in this week's Champions League semi-final.
Hughes, however, advised Bale to stick it out for the greater benefit of his career.
"He probably would have liked to have affected the game more than he was able to but you have to factor the opposition into that - they weren't playing a poor team on the night," said the Potters boss, who had spells at Barcelona and Bayern Munich as a player.
"Sometimes you have to credit the opposition with doing a job on players and I think that maybe was the case.
"He is an outstanding player and has proved that over a long period both here and in Spain - he had an outstanding season last year.
"He has come in for some criticism but that is par for the course at Real Madrid and I'm sure he is used to it by now.
"I have experienced playing abroad myself and I probably went with the wrong attitude of maybe saying to myself 'I'll do it for a year, maybe two, and then get myself back home' - which is completely the wrong way to approach it.
"I think Gareth has every intention to stay out as long as he can
I would recommend that because you shape yourself as a player and a person the longer you stay out.
"If you are at a club like Real Madrid, or Barcelona as I was, you stay there until they kick you out of the club."
Source : PA
Source: PA