You have to factor in that he's in the process of "popping" and moving when catching that ball and trying to throw someone out. That's going to hinder his ability to determine if it's close enough to challenge or not. That ball is right on the edge - it's not a blatant strike.
If he just puts that ball is his back pocket, it's a 1-2 count with the top strikeout starter in baseball on the mound. Even with runners on 2nd and 3rd, he probably gets out of that inning with 0 runs scored like 90%+ of the time.
And for all we know - Schneider might have tightened his challenge leash lately, seeing as he's been pretty bad at it. Maybe they have been prepping them more and reminding Kirk that he's f*cking horrendous as challenging? As if Kirk didn't notice that already? Kirk's kid probably noticed he never gets challenges right. Maybe he's influencing him!
After that entire plays ends, with the disappointment that Kaz can't catch a 14 MPH lop ball - I don't think it's reasonable for Kirk to immediately challenge the strike call, nor is it any managers fault for not having drilled that mentality into him.