If I were to guess, I'd guess that lemmy.ml is falling apart under the load of new and increasingly active users. You can try:

• Wait 5 minutes to see if it sorts itself out. If lemmy.ml is slow to respond to your subscription request this can happen. And it has good reason to be slow right now with the massive influx of users.
• If it doesn't self-sort, click the pending button to unsub, and try resubscribing. It may take right away on retry. I had to do this with a bunch of subscriptions early on.
• Find a few more communities on servers that aren't yet having an existential meltdown under load to tide you over until admins are able to scale up to demand.

lemmy.ml has lagged a lot for me too, so I've avoided its communities. Maybe this is good for spreading the communities anyway.

It might be that Lemmy.ml is busy and can’t keep up.

May I ask why you are subscribing to every instance? Just pick one instance (probably not lemmy.ml) and join the communities from there. They are all federated so you can follow any community on any instance if it is federated with yours.