The Owls silenced the stadium via Jermaine Johnson's opener but were undone by two Luke Varney goals in the space of six minutes, leaving Jones to rue a missed opportunity.
He said afterwards: "We should have won. We switched off for 15 minutes and allowed two goals which we should never have allowed. You can't give somebody free headers in your box.
"It's frustrating because they caused us no hassle, apart from a 15-minute period. We had a few injuries and had to change things around but we made some basic errors.
"Jermaine Johnson had a knee injury - but the referee missed that one. Giles Coke was injured as well - that's why he went off. There were a couple more including Reda Johnson with his foot."