The Potters midfielder scored in the 2-2 draw on 6 October but came off after the break in Vienna.
Allen was ruled out of Sunday's 1-1 draw against Georgia after scans showed the extent of the injury.
"We're still checking on Joe, he hasn't trained with the group yet," the former Wales manager said.
"We would have given him an extra day's rest but he trained with Wales and that's probably compromised him a little bit so they have to be a little bit careful in that regard."
Hughes' side face Sunderland at home on Saturday, hoping to pick up their first win in the Premier League this season, but the Stoke boss hopes the summer signing from Liverpool will be fit to feature against the Black Cats.
"We've just got to be a little bit careful with him; unfortunately he probably did a little bit too much with the Welsh squad," Hughes said.
Hughes later spoke at a press conference about Allen's injury and was asked if the player would be fit to face Sunderland.
"Joe Allen is doubtful, but we are hopeful on him," replied Hughes.
"He has had a bit of discomfort, which is probably down to the workload he has put in.
"He has had a busy summer and is now playing week in, week out, which maybe he hasn't done for a while.
"You can see the amount of work he puts in on the pitch, so we have to be a little bit careful with him."
The Football Association of Wales declined to comment when contacted by BBC Wales Sport.
Stoke City manager Mark Hughes says Joe Allen was "compromised" on Wales duty after he picked up a hamstring injury in their draw against Austria.