Nice write-up Falanca. I didn't really get so many of these problems in the first two episodes, but in the 3rd several of them hit me!
Let me just add a couple of things to your list:
Episode 2: The Tomb of Sammun-Mak
1. Sometimes, the Can-o-Nuts would be visible on the tray during the cutscenes of Kringle poking his head out of the door, even tho Sam and Max were still stood there. This basically spoiled the solution for me because it showed me I was going to use the can there! This comes under "spoilery glitches" rather than "auto-solving".
Episode 3: They Stole Max's Brain!
1. Noir/interrogation. Don't get me wrong, I *loved* this sequence. But it got kind of spoilery due to used options getting grayed-out. After I'd gone through all the sequences several times and used all the options, everything was grayed out; then when I found out some new information the "You're lying!" option would suddenly be in white again, so it was obviously the new option. Working through dialog puzzles just by seeing which options have been used and haven't made me feel like I wasn't actually solving a puzzle intelligently.
The other problem that sometimes happens (and in other dialog sequences as well, not just noir) is when I'm trying to pick the wrong answers, but accidentally I stumble on the right one! This happens sometimes when puzzles aren't totally logical, I can't think of a specific example but it did happen once or twice in noir.
The grayed-out dialog options are generally quite useful when you're trying to get all the gags out of a normal conversation, it helps avoid repeated lines. But I think when a puzzle is centered around dialog it can help a bit too much.
2. Museum. I tend to wander around and click on everything... so I didn't realise the significance of having to use the monster diaorama to hide it before I set up my own fake one; it was either hidden already, or a game glitch made it irrelevant.
3. Corn dog pyramid. The only puzzle I actually got stuck on in this game was the credit card. Basically, because I'd already used the corn dog pyramid to get toasters banned, I assumed that would be the only use for it. I was trying to work out how I could get the card directly off Frankie, or somehow substitute Max for his card, or something like that. Telltale don't usually repeat puzzle solutions like that, so I really wasn't expecting it. When I read on the hint forum "you have to make credit cards illegal" I was like OH *facepalm*.
4. Skunkape fight. I should add that I didn't even see the molemen help at the end (I was expecting them to be involved somehow and was looking for it, for whatever reason I just didn't even see it happen, again it's possible that a game glitch meant I won the fight even though the molemen had actually been zapped by Sammun-Mak). So I was left at the end feeling confused about the purpose of a whole bunch of things.
Overall I think some of the puzzles in this episode lacked the depth we're used to in Telltale games. I think basically by taking the inventory away, it's result in lots of "click on this to get an effect" centric puzzles. Certainly an interesting change, but it means there aren't enough different combinations of things to try. Inventory items are kind of an instant multiplier of possibilities, making it much harder to complete something by accident!
It's started feeling more like watching an entertaining cartoon, than actually having much to interact with and solve. Except I have to spend ages clicking through all the options to find the good gags, whereas on a TV show they're just served up to you. It is still highly entertaining of course! But I think with new puzzles based around dialog and superpowers, you still need some inventory in the mix to vary the options.
P.S. If I've written a long post, I usually just press CTRL-A then CTRL-C to copy the whole thing to memory before I submit it. Then I can just CTRL-V to paste it back in if there's a problem and it gets lost! This happens all the time on all kinds of websites, so it's a good habit to get into. It's saved me from tears on more than a few occasions