I'm guessing Klentak didn't know. He pitched on Friday, they probably figured he was a little sore, and at that point they didn't plan on ILing Segura (let alone lose Kingery). It says the Phillies had decided "earlier in the game" that Arano couldn't go. Can't make a roster move at that point. He probably hadn't fessed up about how bad he felt. I still think he's probably not really injured, "inflammation" from a week-old massage is something you ice, maybe take a day or two off. But they couldn't afford to do that (plus it allowed them to get Anderson, and not forcibly IL someone who wasn't even "sore").
So yeah you can say Gabe screwed up, though I don't think you ever manage for the 12th inning (and someday soon you won't have to). But also I don't think we can say it was obvious to let Seranthony bat in a 2-2, game, top of the 7th, man on second base, two outs. Williams hits there and you don't have extras. And obviously if Franco hadn't gotten on Seranthony would have stayed. Double-switch probably not much of an option with Kingery and Segura and Cutch already out, would have meant putting Williams in CF or pulling Harper probably.
And Nicasio still should have won the game. He didn't lose it because he was tired, or even bad. Sounds like Gabe and JT were as much to blame for that fastball, in fact.