"Subscription pending" means that lemm.ee has registered your subscription, but the remote instance has not confirmed it. This can happen in one-off cases when there is some network issue between lemm.ee and the remote instance, but if it's happening for a longer period then it might mean that the remote instance is down or otherwise having trouble.

One thing to check for: is the remote instance running 0.18.1 or later? Earlier versions of Lemmy had serious trouble with federation.

If the remote instance is on a fresh version but still having trouble, please list some specific examples of communities that won't accept your subscription and I can take a closer look!

You can completely ignore this and don't have to worry. "Subscribed" and "Subscription pending" both mean you are subscribed to the community and posts from the community will show up in your Subscribed feed either way. The only difference is that "Subscription pending" basically means that your subscription status for that community has not been 100% synchronized on other instances across the fediverse. This doesn't affect you at all (you are subscribed to the community either way) and I think this is something that will be less confusing in a future Lemmy update.