So the answer to your original question is yes, some instances are closed off from others, but you didn't mess anything up. Instance A can "defederate" from Instance B, which makes it so that users of either instance cannot see or interact with content or users from the other instance. This is unilateral- even if Instance B does not defederate Instance A, it is still blocked from seeing or interacting with Instance A.
However, with regards to your later questions, you didn't mess anything up. It's simply that federation is not retroactive. When the first person from Instance A subscribes to something from Instance B, the two instances are then federated, and content begins being shared from that point forward. It does not retroactively add old content from Instance B to Instance A. For now, it matters relatively heavily, as instances are being federated constantly, even though the content flow is somewhat light. As content flow increases and new instances begin to stabilize, it will matter less. As time goes on, the content "before federation" will be vastly outweighed by the content "after federation".
This is all somewhat compounded by the fact that lemmy instances are absolutely slammed right now. Kbin.social had to defederate entirely for a while just to keep from crashing. Give it time for the spike to stabilize and it will work more smoothly.
Nah, there are still a lot protesting, they just know that if they don't do things a certain way they'll be replaced with bootlickers. Pics, gifs, aww, interestingasfuck, iOS, wellthatsucks- all are bringing attention to the admin's bullshit while technically doing as admins asked.