Rangers twice led the match before losing 3-2 to Reading at Loftus Road as their cup run was brought to an end.
Despite not being too downhearted by the way his side played, Hughes is annoyed to have conceded the goals that they did.
"Obviously at 2-1 I felt we were in the ascendancy and had done enough, but it was an outstanding free kick from Shorey, which he always has the capability of and at 2-2 it was anybody's game," said Hughes.
"We are disappointed with the manner of the third goal because there were too many consecutive errors that led to the lad having space and time to be able to backheel it in our six-yard box.
"To lose it in that manner is disappointing but it is understandable to a certain extent given the changes and the injuries we have at the back. We haven't had that continuity at the back, which you need to bang results out."
QPR host West Ham United in the Premier League on Monday.