Martin Hunter said Southampton were punished for a poor second-half performance in their Checkatrade Trophy defeat to Reading.
Saints were knocked out of the tournament on penalties at St Mary's, after a 1-1 draw in the last-32 tie.
Hunter felt they should never have allowed the game to reach a shootout, though, having dominated the first half and leading through Lloyd Isgrove's superb goal.
"The penalty shootout is frustrating, but my biggest disappointment was the second-half performance, so we shouldn't have even been in that position," he said.
"From playing quite well in the first half and obviously taking the lead with a very good goal, we spoke about several things at half-time, one of which was about how we started again and the danger that they posed from set plays, and obviously that warning wasn't heeded.
"I was pleased with the first half, but when you come in at half-time and it's one-nil you know the opposition are going to come back at you, which they did, but the second half is really our downfall. We never got going. Our general play, individually and collectively, was below the standard we normally expect."