These days, I see a lot of games making the same mistake. I think this mistake is only really possible because of changes in technology, because I'm sure it would have been made decades ago if it were possible back then.
The mistake is trying to be cleverer than your players.
This is a difficult thing to discuss, because in nearly every case you are actually going to be considerably cleverer than your players. Not because of any innate cleverness or stupidity, but simply because you can see everything and have spent a lot more time on it. So there is an urge to leverage that.
But it never works out. In trying to be cleverer than your players, you inevitably end up being annoying. Instead, try to be clever with your players. Instead of getting in front of them and showing off, get behind them and push.
The simplest example of this is the concept that you need to "punish" your players for playing badly or wrong. That's not a very good concept. Players never need to be punished by you. Ever.
Players do need a system of reward and punishment, failure and success, yes. But here's the thing: it's not you, the designer, that needs to punish or reward. Instead, think of your job as helping the player figure out how the game rewards and punishes.
Let's start giving examples!
In Rune Factory 4, along with many other games from Japan, the game is structured with a simple save point system. With saves before every boss, the game is obviously intending for you to try the boss again and again, loading from the save until you get it right.
But the developers of RF4 have decided they should "punish" the player for "failure", so instead of asking you to load a game when you die, they resurrect you back at town. For a huge fee. This is an inferior option in every circumstance: not only does it move you out of the deep dungeon, it also costs you time and money. You start the game with an "escape" spell that can get you back to town instantly anyway, so there's not even any advantage to that aspect of it. It is simply a punishment that the developers have decided to inflict.
To try to force you to accept their punishment, they actually remove the "load game" option from the game. You can only load from the title screen, and there's no way to quit to the title screen. Unfortunately, the punishment is so severe and runs against the grain so badly that you'll end up force-quitting and rebooting the game to load it like you intended.
Now, the problem here isn't the punishment itself. A punishment for dying is fine, but it needs to be part of the structure of the game.
For example, in any given Mario game, you certainly die. And there is a punishment - starting from the checkpoint or even getting kicked out to the world map. This does not make Mario hardcore or difficult. It's just a failure or success built into the structure of the game.
Moreover, the developers are always careful to try to set you up to understand how the punishments and successes are going to arrive. Challenges are often predated by an earlier "prep" challenge of the same type but less difficult or lethal. Rewards are set up so that you almost have to get them the first time you see them, just so you understand that getting them results in something good.
In games which are difficult, such as Kerbal or Dark Souls, failure is often quite stark and punishing. But the structure of the game revolves around that. The game is hard. The developer is on your side - even in Dark Souls, the developer is on the side of the player. Always dropping little clues, hints of what challenges await, the resources you might need. In Kerbal, the developer is more hands-off because there's not really any level design, but the forgiving "revert to launch" function essentially allows you to undo any mistaken missions.
That's how you design a game. The game rewards and punishes. The developer sides with the player against the game.
It's certainly possible to take it too far. For example, I recently tried to play a Mario game on my 3DS and found it to be unplayable, because every time I died a few times trying to get a particularly difficult collectible, the game would force me to take an infinite-flight invulnerable coin-creating tanuki suit.
This goes beyond siding with the player and straight into destroying the entire game. This would be like if you died 3 times in Dark Souls, it gives you the ability to fly and invulnerability. It subverts the structure of challenge, reward, and punishment. That's bad game design.
Here's another type of example:
There's a fair number of games where the developer obviously takes their game quite seriously, and seems touchy about letting the player goof off or be silly. If the player tries, the game punishes them.
Take something like COD Ghosts. If you stop for a moment to look around, you fail the mission. If you walk the wrong way, you fail the mission. If you interact in the wrong way, you fail the mission. The actual structure of the game doesn't contain any of these punishments: fundamentally, the only rewards and punishments built into the gameplay are those of shooting and getting shot (or sneaking and getting caught, etc).
But the dev adds in all of these additional restraints, either because they are completely full of themselves or because they think the player is deeply, deeply stupid. Well, whatever the reason, the result is that the player is not allowed to play in the game. They are only allowed to play through the game.
Contrast this to a game like Mass Effect. ME's missions are just as confined, but the confines of the mission are built into the level design - they are part of the structure of the game. You very rarely run into any arbitrary "you fail!" conditions. In turn, this means that all of the Mass Effects were entertaining to play in rather than just play through. Halo was like this as well.
If you want to experiment with grenades, go ahead. If you want to stack your party members on top of each other until they resemble a monster with four arms and four legs, go ahead. If you want to try to take on the whole mission with just a pistol, go ahead. The developers are on your side: if you come up with something you want to try, they go "oh? Sure, go ahead!"
Not only does this freedom allow players to play in the game, it also allows players to create new kinds of play - such as beating the game solo, or with an all-biotic team, or never equipping any armor, or whatever.
Now, Mass Effect comes with a huge amount of dull, pre-scripted content that it forces you to push through. All the renegade/paragon options, the badly written dialog with obvious endings, all that stuff is not really gameplay. It's the same as COD Ghosts' restrictions.
So they added in triggerable events - renegade or paragon interventions which radically change the flow of the conversation. And even though these, too, are carefully pre-scripted, they really spiced things up. Why did that work?
Well, the whole conversation thing was sculpted so the player would think of everything in terms of paragon or renegade. So when the conversations got sluggish, the player got annoyed and knew they were just going to choose paragon or renegade and impatiently waited for the chance to choose. The flow of conversation was extremely predictable and dull, and the choice was extremely predictable and dull.
The devs heard the players and let them express themselves much more quickly with these paragon/renegade action cues. The devs took the player's side to help them within the framework of the conversation. In doing so, they actually improved the conversation mechanic dramatically: now the flow of the conversation was always spicy, because the player knew that at any moment they might get the option to kick it in the face.
The conversation mechanic is still pretty dull, of course. The actual amount of player agency is pretty low. But it's way, way better than just an endless conversation tree.
Side with your players. Help them play your game in the way they want.