As Uglies shows us, the worst confinement isn't being kept in a small rabbit pen or chained to a desk in the Shmoop basement writing guides. The worst form of confinement is that Tally's society prevents people from finding their identities. (Although being handcuffed by the Specials and put into a rabbit pen is also no fun.) In Uglies, people are confined in their choices or are pulled in so many directions that they're not really free. Like Tally: she's stuck between her conflicting promises to Peris and Shay; Dr. Cable's blackmail; and her growing love for the Smoke and David. People in Uglies are trapped because they're stuck in a system they can't get out of.
No character in Uglies is really free. Even the ones who live in the woods.
The most limiting confinement in Uglies is self-imposed: it's when characters won't allow themselves to change or grow or compromise.