I do have something similar - Nostr clients all seem to have different ideas of the number of users following and users followed.

Example, on Primal, I follow 67 users and I am followed by 40.

On Snort, I am followed by 3 of myself (somehow) and follow 9 people.

But then, nostrudel has me following 60 users, and followed by none.

As for solutions, I'd say try and stick to one client for a longer period of time, and try different relays.

Would be nice to have a built-in client-side option to force a "Query Network" and update based on that (which itself could lead to issues).