Normally video gamers can ignore most of the story and player through a game and win. No matter what betrayal would happen, they just need to be skilled at completing objectives. They understand this and aren't really concerned about the betrayal except for maybe the equipment they might lose. They passively listen to the story as listening to the story doesn't provide any gameplay benefit.
So what happens when you give that same player real choices and NPCs that tell "white" lies that could be fatal? This presents a lot of unique game design problems as you have to solve at least a few of them to make the game enjoyable.
Issue #1: Players not figuring out that lies even exist or that they can do something about them
Players are so used to blindly following the objectives given to them that some of them will just believe anything that the NPCs tell them. Even if you get another NPC to say something like "Don't trust them." It doesn't exactly tell the player that they can do something about it. At most they'll strip that untrustworthy character of all their gear. Then they'll wait for the betrayal.
In Fading Hearts after every ending, there are some commentators that give the player feedback on how they did, what they can improve on, and some hints of what to do next. Having an unexpected ending (Ryou may die) that will occur if a player chooses to blindly follow what the game tells them helps when combined with the post-playthrough commentary.
Issue #2: Difficulty of Designing Lies (or fatally inaccurate truths)
How do you design a lie that is critical for players to figure out? This actually is a bit more of a probablity problem in the general case. Combined with where you put the hints (or lies), how believable the lie is, and how strong the hint is makes for a complex issue filled with a lot of creative potential. The risk is where the player might get stuck or not experiece the greater parts of the story.
Here is an example of an inaccurate truth that helps illustrates this issue.
Issue #2: Playthrough #1 example
There is a legend about a legendary healer and legendary knight. The healer has the warmest heart and the strongest healing and support magic. The knight has a fighting spirit, a will to protect and the greatest swordsmanship skills. They will join forces to defeat the evil lord in a grand battle. The kingdom has found them and sends them on their journey to defeat the evil lord.
The knight is always kind to children and always wants to help. His skills are unmatched in the battlefield however. The healer wanted to become the legendary healer and she was fiercely competitive in her magical school. The player expects a twist soon involving their roles.
Eventually the Legendary Heroes defeat the Evil Lord and all is well. The boss seemed a little hard even for a final boss.
It seems a bit off or cliche. There's also a plot thread that seems to go nowhere. For an interactive storyline, it's required.
Issue #2: Playthrough #2 example
Same beginning only now the heroes hear about the Legendary weapons that only the legendary heroes can wield. They seek them out and find the sword for the legendary knight first. The knight tries to pull the sword out of the stone but cannot! The knight loses his will to fight for awhile but then resolves to guide the legendary healer to her legendary weapon.
They get to healer's legendary weapon. She cannot pull the magical staff out of the stone either! They get really discouraged at not being the chosen heroes.
The player can still continue on to the rest of Playthrough #1 story. If the player has been paying attention to the story, they might try to get the knight to pull the staff out or the healer to pull out the sword. Then they will find that it works! Then the heroes will unlock their true powers.
You can see the issue if the player doesn't figure out that there was something they can do.
Issue #3: Why should the player try to foil the lie?
When a player figures out a very well-crafted lie (or inaccurate truth) , they should get rewarded outside of the story as well. In the above case, it's a lot of powerful abilities that they would not get otherwise. There should also be a boss that would be very difficult without the weapons and an alternate ending.
Just making the story interactive isn't enough at times. You can create a compelling story but there are a lot of design issues just to allow the player to do something about them.