-Wakanda rejected the mutant nation because of how it was being formed. Basically it is take our flowers and accept us as being nation. Wakanda said no to that they don't need flowers they are already advance (and unlike Krakoa they have been keeping all the improvements that can help the human race to themselves).
- Wakanda and Atlantis were the two nations that back Jean Grey in X-men Red when she was putting together her mutant homeland. Proving Wakanda isn't against mutants having a homeland/nation but how they presented it.
- Krakoa just put up a broad warning internally,basically anyone who rejected the offer is potential hostile. And based on what happened in Russia(sending mutants to Gulags),North Vanion(blocking the gates) and Brazil(mutant attacking animals released) pretty much every country that rejected the offer has been up to no good. Krakoa is with in good reason to have a posture that Wakanda might be potential dangerous to them.
Both Countries made moves not of malice but to just cover their bases. This topic takes wild reach for something that isn't there. Xavier isn't going to try to destabilize Wakanda because they aren't mistreating mutants . The mutant cells and destabilizing was for the countries that are trying to keep mutants from joining Krakoa. Anyways I am proud of the X-men franchise for once because for the first time the X-men aren't just running around saying peace and praying it works. I love in addition of doing things the "right way" they are also hedging their bets and willing to do a little dirty work for the great good.