The Students' title defence was hampered by injuries to key players such as Buhle Mkhwanazi, Thulani Hlatshwayo and fellow defender Nazeer Allie, and swiftly crumbled.
However, they still managed to win the Telkom Knockout and have eased their relegation fears on the back of a six-game unbeaten streak in the league.
Hunt's side picked up three welcome points with a 2-1 win over struggling Golden Arrows at Princess Magogo Stadium on Saturday courtesy of goals from Gabadinho Mhango and Lehlohonolo Majoro.
“We have been stable the whole season but it has just been through injuries,” Hunt told reporters at the same venue they won the TKO.
“When we played Golden Arrows [where Wits lost 3-1] in the first round, this team that played today, we had eight changes and look at the one we play... you tell me. We never had players, we never had the squad, they were all injured.
“It’s how football works but we can’t complain about it, we got to get on with it.”
Meanwhile, Hunt was unimpressed that Wits striker James Keene was sent off by referee Victor Gomes in added time along with Arrows' Jabulani Shonge. Keene went to stop Shongwe from dragging a prone Mhango off the pitch as the clock was winding down.
“I don’t know. When you are losing players like for that. If you losing for that, I mean I ... don’t know. Anyway.
“It’s crazy. Anyway.”
Hunt's men next face Pamplemousses in Mauritius on Wednesday in the preliminary round of the CAF Champions League. The Clever Boys won the first leg 2-0.