In 2018, there was a surge of accounts about Nigerians travelling through the desert to get to Libya so they can migrate to Europe as well as getting entangled slave rings while in Libya. Just days ago, 160 Nigerians were repatriated from Libya. So, it's understandable that individuals with questionable or unclear motives for wanting to travel to Libya are rejected.
2. South Sudan
South Sudan doesn't offer visa-on-arrival for Nigerians. You have to visit the embassy and apply for a visa like any other foreign country, and if you don't have the appropriate documents or reason for travel, you can get rejected.
Botswana is a country famous for wildlife experiences in the Southern part of Africa. To travel here as a Nigerian, you need to apply for a tourist visa. In fact, their official website says: "All Citizens of Commonwealth countries do not require visa except those from Bangladesh, Cameroon, Ghana, India, Nigeria, Pakistan, and Sri Lanka." So...
Out of the many African countries that do not need visas to travel to this small land-locked country in South Africa, Nigeria is NOT one of them. You need to apply for a tourist visa at their embassy too.
Namibia has actually jumped to the top of countries Africans want to explore. However, as a Nigerian traveller, we can't say the process is exactly easy.