Wits battled all the way to extra-time before they crumbled to a 5-4 defeat after a penalty shootout at the Tsakane Stadium on Tuesday evening.
With nine changes to the side that beat Platinum Stars on the weekend, Hunt was left unimpressed by the players he showed faith in to do the job on the night.
"It's difficult to play against Cosmos, we knew what we were up against and all credit to them – they did what they had to and got through," Hunt told SuperSport TV.
"Tomorrow, no one will remember how they got through but that they did so. I don't know how much possession we had in and around their box, but a lot of players that I gave a chance to weren't there tonight.
"You learn a lot about people when given a chance and they don't do it for us. So we'll regroup and start again but I'm very disappointed because I thought we did enough to try and work [our way through].
"It's always difficult to play against Jomo [Sono] and we knew that, so we should have been better."
Hunt made two changes at half-time, hurling off Ejike Uzoenyi and Jabulani Shongwe for Phakamani Mahlambi and Daine Klate, and the Clever Boys looked a completely different outfit in the second half.
"I changed the shape at half-time to try and go a little bit more direct, which worked. I mean they never came into our half in the second half," he added.
"It's just that final ball that we couldn't get in there but we had to be a little bit better, more crafty, more inventive with our inter-playing.
"Phaka [Mahlambi] did great, he goes past the first man and then he's got to pass it, but he did great and changed the game for us in the second half.
"Disappointed because we wanted to stay in the cup. Now we've got CAF [Confederation Cup] and you know we play every two/three days so it's tough."
Wits next face Egyptian side Smouha in their CAF Confederation Cup play-off first leg clash at the Bidvest Wits Stadium on Saturday.