High-profile appointment Hughes lost on his first game in charge last Saturday against Mansfield, and it was a similar sinking feeling this Saturday as Swindon win 2-1 at Valley Parade.
Gareth Evans opened the scoring for the Bantams after 18 minutes but Harry McKirdy levelled three minutes later.
Jack Payne then broke City hearts with a penalty six minutes into added time at the end of the game to give Swindon all three points.
Harrogate Town were punished for a lack-lustre performance at home to Hartlepool United, going down 2-1 at Wetherby Road.
Leading marksman Luke Armstrong fired the Sulphurites into a 21st-minute lead against his former club, however the visitors were the better side for the majority of Saturday afternoon’s contest and deservedly fought back to take all three points.