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The Canadian had only just returned to action as a second-half substitute in his side's 2-1 win over the hosts at Easter Road.
It was his first appearance for the club since August when he played his part against Kilmarnock before a hamstring injury forced him off at Rugby Park.
Johnston lasted just 20 minutes against Hibs before he was forced off again and manager Martin O'Neill admitted at full-time that a recurrence of the original issue cannot yet be ruled out.
Lennon, speaking as part of his punditry duties for Sky Sports, claimed the staff were perhaps premature in greenlighting the Canada internationalist the chance to play a part in the action.
And he hopes the 28-year-old does not suffer further.
"I don't understand it. This isn't the first time this has happened to Alistair, so I don't know what is going on behind the scenes," he said.
"You know, the medical team, the fitness team and the coaching team have felt that he is fit to play some part in the game - but quite clearly that has not been the case.
"For me, Martin obviously can't diagnose it straight away and what the damage is - if there is any - that has been done. I doubt it's a psychological thing, knowing Alistair Johnston, he is obviously feeling something is not right.
"I don't know if he needs a prolonged period...hamstring injuries are such a difficult one to get right - the rehabilitation right and the timing right - you can do it again. If this is a reoccurrence if the same injury then that is a real, real worry for the player."