I also solved one side by random fiddling, then got stuck on the others without any idea what the logic of it was. But I figured I was just being dim, Eventually I had to look it up in a walkthrough.

I got stuck a few other places as well (I suck at adventure games):
I didn't understand why I couldn't just go to the graveyard. All the other locations relevant to the investigation showed up automatically. I thought there was some other part of the game I had to complete first. Having to discuss a LTM first didn't really make sense to me.
I also couldn't figure out how to get the FTTN number from the Antevorta database, because I assumed I couldn't do it while the receptionist was there, so I was trying to find ways to get her to go away again. Talking to her about the mainframe (as Ray) didn't come to mind.
I thought I had to hack the security code on the police archive system, I didn't think to just have officer Johnsen do it for me. While in the other cases I felt I got stuck mainly because I didn't "read the designer's mind," so to speak, I really should have got this one. I had all the pieces of the solution, I just didn't have that creative insight. (Love the social engineering aspects of the hacking puzzles, by the way!)
I couldn't find the magnet in the police tech room. That seemed like just a pixel hunt. Gah! Only asking the other character for clues gave me any indication that there was anything there for me to take at all.
Finally, in the phone tracing puzzle, the tips from Bennett made me think I just had to keep the conversation going until all the dialogue options (both aggressive and interrogative) were gone, and I tried and tried over and over, but even with only the two-three that would always end the conversation left, it never worked. The walkthrough I found provided a sequence that worked, but I am still not sure what the logic of the puzzle is. One of the options will get him talking, but only if you've done certain of the other options first? What is the relationship there?
Oh, and there was one thing I never figured out the use for:
I didn't have that much trouble with any of the supposedly difficult mini games or logic puzzles, though. I think because they don't really require you to be particularly clever, just methodical.
I did come across one minor bug:
All that said, I loved the game. In many ways it's as if you made a game with only my favorite things about adventure games: excellent design, a compelling story, low key humor, and plenty of varied, fair puzzles - all executed with impeccable polish. I was only half joking with the question about your next game, because I really hope that, having made your magnum opus, you haven't had enough of adventure game making. You know that "spare time" and "personal life" are overrated, right?!
But congratulations on how successful and well-received
Resonance is, Vince. It's well deserved.