Well, I haven’t used a lot of twists yet, but damage or penalties is fairly rough. Even min damage can be 3 or more which is 10% of a player’s health.
Also, a penalty can mean that they are more like to get a worse twist the next time, which can spiral.
I’ve also seen between 2 and 8 minions added to a scene because of a twist. This skews the battlefield very much in the villains favor, causing more damage, more hinders, and may slow down achievement of the main goal. Same with Lieutenants, though usually that is just a single lieutenant.
In a similar vein, you can end up with a new overcome challenge, such as civilians in danger or a doomsday plot and that can delay the characters significantly. I actually did use this once and got the people involved a little miffed, because a major twist let to the villain having wired the place to explode, and the characters had to deal with a suddenly much different scene than they were in before, and nearly didn’t make it in time.
You can also lose access to your powers or qualities for an entire session, losing the main way you interact with your character, such as a fire character losing their fire powers is fairly devastating if it happens early on. Great RP potential, but it presents a line that is tricky to deal with.
Yes, twists aren’t bad. Twists can be great and the examples you gave are great uses, but there are also many many uses for twists that can lead to the team getting delayed to the point of failure. Especially if you are triggering twists more often than usual, and end up triggering a spiral.