Well it's one of the lower stats and the only thing close to offensive magic is Magic Field, a somewhat paralyzing effect that summons a cute puppy that rampages wildly. However Endure is defensive magic and should have been easy to work with. The MC literally uses it to play with fires so the first sign of fire should have been instinctive.
but not a trained fighter
We train with ninja girls, some of which actually wanted to kill him. It's also safe to assume Gramps hasn't neglected the boys training since he survives training against those Kunoichi and possibly gets his dick wet as a reward.
so he hasn't trained an instinct on how to deal with an unknown threat
We've let goons kidnapped him, almost drown him, set him on fire, arm wrestled minotaurs, sicked abominations on him, and sent him into the dark abyss to name a few things. By now it's not so much unknown as it is can we stick our dick in it.
At some point when bad things keep happening to the MC on a regular basis one might expect a bit more preparedness.
Cautious Hero: The Hero Is Overpowered but Overly Cautious
"Oh no, when I gave her instructions before I didn't tell her to do this other thing!"
We also didn't tell her to take baths, use the restroom, or eat and drink for that matter. Girl has some natural instincts.
Original Chloe also has shown internal monologue of wanting to protect her sister and the AI probably wouldn't prevent that as long as it was in the MC's interest which that is.
Some of the silliest examples I've seen in other games are where a frame is supposedly showing something flying at someone's face (say, cum), and in that frame they have time to think entire sentences even though the next frame with it hitting their face would logically happen a fraction of a second later.
Time is always a thing and hindsight can be a bitch
But hear explosion, tell Chloe to protect Alice (A command similar to Act 1 "I'm not leaving you to die!" choice that funny enough gets ignored), cast Endure, go see what that explosion was about.
If things go south then call Chloe but leaving the little girl behind and expecting her to not check on her big sister was idiotic.