Other logic flaws I've noticed:
Eliza's outfit has always been shown with black panties, somehow has white panties at the lake.
Talking your way past the guard: Made no sense. The Guard, if he was actually worthwhile would have said something like "I don't care what your business is, the gate is closed until further notice." or "If you actually have business with the Guildmaster, I'll send word to him and ask. Wait here until then." Not "Oh sure, that flimsy excuse is fine. You don't need a pass, go ahead." Edit: Later Flynn, Sabrina and Alice get in without getting stopped. WTF?
Luring the Wolf Away: First adventurer's guild quest lets you lure the wolf away and befriend it. Selena somehow says that the problem is now solved but without any kind of proof that the wolf is actually taken care of and nothing for Eliza and (Noah) to take back to show they did something with the wolves. He also never explains to anyone what he did. But somehow the situation is resolved, apparently. I know the whole thing was used to introduce Rin and that she'll probably show up later, but god damn was that dumb. At least make him explain it to others so they know the wolf won't come back. LOGIC.
Adventurer's Guild afterwards: Dalen knows Oren sent (Noah) but neither he nor Eliza ever said it. I was actually waiting for it in the original conversation with Dalen but it never came up.
Goblin Quest: Neither Eliza nor Noah have weapons. They go on a quest to kill Goblins. How do they expect to kill them exactly? I get him, but how is she supposed to? When I saw Borri selling weapons I thought "Finally, some logic, a weapon for the girl without magic" but nope. Not to mention the Guild not telling every bit of information (about the Beserker) they had with Dalen giving the flimsy excuse of "They won't always have all the information for every quest" is a bullshit line when it's the Guild's responsibility to make them as prepared as possible so they don't get killed. What a load. The writing is getting worse as this goes on.
Later: Ok, somehow she now has a dagger.... that she has never had before.... in any of the fights she's been in....
Back at the Guild: Eliza and Noah bring back trinkets. But nothing to show they actually killed the Goblins. If Sylph hadn't been watching, she'd have no way of knowing if they were telling the truth or not. So yet another quest paid out with zero proof it's actual completion. This is aggravating me, have you never read an isekai manga? Proof is always required.
Also Dalen is finally told about Oren.... long after. Ugh... this needs a massive rewrite to get it's order of events sorted. Also Eliza asks "Wait, you knew my father? How" But Noah had told her previously he was going to the Adventurer's Guild to see Dalen because Oren sent him there to see his old friend. So now we know Eliza has the memory of a Goldfish or the Dev can't keep track of his own script. There was even a spot where Noah mentioned to Eliza about being a Nephilim before they reached Riverside, but then doesn't actually have the conversation about it until after they leave. I brushed it off as a single mistake, but it's clear the dev needs help keeping his story in order. This is just getting dumb.
Please note, I am not making these complaints to shit on the game. I'm complaining because this story is great and the VN is fun and worthwhile.. The art is wonderful and the scene direction is some of the best I've seen in a fantasy game. But these story flubs keep annoying me to no end and detract from how amazing it could be.
Edit: I deleted my Selena complaint after seeing later on it actually being part of the plot. Also why is Eliza putting on her gloves and boots before her top and pants... Who raised her?!