Everton striker Nikica Jelavic was linked with Stoke but the Croatian striker opted to join Steve Bruce at Hull.
Hughes admits he has missed out on other options too but is hoping for better luck in the second half of the January transfer window.
"We felt we were close on a number of occasions prior to the window opening and we thought we would get our business done very quickly," he said.
"You get close then all of a sudden you wake up one morning and you find the deal you think is on the table has gone somewhere else.
"So that's happened to us on a number of occasions."
Stoke signed Stephen Ireland on a permanent deal and that allowed Manchester City's John Guidetti to join the club on a loan deal.
Hughes expects the Sweden forward to grow in confidence in the coming weeks, but does not want the additions to end there.
"We're still in the mix for a number of players," he said.
"Given we haven't been able to get too many over the line we've done a good bit of business in terms of Stephen signing permanently, and that's allowed John to come in and we're pleased with that.
"But we still need a little more in that final third, to give us a bit of impetus and a bit of pace to really force teams."