You know what, the game is full of instances of this. You can find a nice list containing some of them right here.
Let's try this one: Bob gets murdered, and Curtis sneaks quietly into Paul Allen Warner's office - while a police officer is talking onto the phone. Curtis sees a piece of with three words on it. Curtis takes the paper and quietly sneaks out of the office. A question could be raised on how this piece of paper ended up on the floor at that time, to say nothing to why the cops did not notice it or take it. Another question could be raised on why Curtis should take the piece of paper. Paul Allen Warner oddly enough does not seem to notice its absence, and he should, because Curtis discovers that the three words are passwords to decrypting three confidential emails in Paul Allen Warner's account. One of the emails has Paul Allen Warner saying that security to the lower parts of WynTech needs to be increased and to kill any intruders they catch in there. Except for Curtis Craig - he is a special case, and if he gets caught down there, then he should be taken somewhere where he cannot hurt himself or anyone else. All that would be fine, except when Curtis finally gets to go down to the lower levels of WynTech, there is absolutely no one down there. He even finds a toy that he supposedly played with as a child in one of the hallways. This raises a question on why no one seems to notice the toy down there for all these years, as well as why anyone would let a child play with a toy in the hallways and right next to a room where a very illegal, immoral, secret science project is taking place. This should demonstrate a number of the numerous instances of Fridge Logic in this game. Whoever wrote the script should have consulted with a professional analyzer of storylines.
Here's another one: sometime after Bob's murder, you get to look into his cubicle and discover a button that had apparently fallen off his coat. Not only can you take the button, but you actually need to take it so you can show it to Dr. Harburg, open up a new branch of conversation, and move the game forward. This raises a question of how the police missed that button and why they did not take it into evidence. It also raises of question of why Curtis would check into Bob's cubicle and take a button that fell off of the guy's coat. Another question raised is why he would need to show a coat button to his therapist just to open uo a new topic of discussion and make the game progress forward.
Of all the people killed in the game why didn't the Hecatomb ever go after Paul Allen Warner? AKA the guy who is actually responsible for shoving him through the portal as a little boy, condemning him to a Fate Worse Than Death. I get that it probably is only growing in power in our world now that the Threshold Project is back online, and it probably needed PAW for that. But now that it is functional, and the Hecatomb is motivated by petty revenge (it hates "Curtis" for replacing it), wouldn't Warner be on The List? Killing Warner would even play into its goal of convincing Curtis he's insane, as Curtis dislikes PAW at least as much as Bob, and would certainly believe that he might have killed him.
A possible explanation is that if PAW were murdered, the Threshold Project would likely get shut down prematurely, which would make the Hecatomb unable to interact with the real world anymore. He's likely saving Paul Allen Warner for last.