The champions are still chasing their first league win of the season as they were foiled by Siphelele Mthembu's late equaliser in Bethlehem on Wednesday night.
Johnstone, who was overseeing Wits in the absence of suspended head coach Gavin Hunt, felt the Students should have done better with their numerical advantage following Thamsanqa Teyise's 68th minute dismissal for a second bookable offence.
Johnstone told SuperSport TV: "Obviously with them going down to 10 men it was our game to lose essentially. We were pushing and pressing, and doing the right things but again nothing really fell for us.
"Again we failed to convert chances, even though we scored two tonight, we still conceded two. We certainly have to be better offensively and defensively and there's a lot of work to be done."
He added: "At the moment we can't buy a win in the Free State. We have got to look at the whole. In the last couple of seasons we have really struggled down here. There is a lot to work on, a lot of negatives but we got a point away from home and we'll take it."
Meanwhile, man of the match Kobamelo Kodisang was thrilled to force a goal with an intended cross on debut for the visitors.
"I felt good, it was a team performance. I'd like to thank God upstairs and I'd like to thank the coach for giving me a chance and believing in me," said the former Platinum Stars attacker.
The Clever Boys, who lost their Premiership opener 1-0 to Cape Town City, will meet the Citizens again in the MTN8 semi-finals in Cape Town on Sunday.
Hunt and new signing Slavko Damjanovic will be back for the game after serving a two-match suspension following their red cards in the MTN8 last-eight win over Golden Arrows.