For some reason, on some systems the server requires a "scope" like "%eth0" in order to bind to an IPv6 address. The driver can parse an IPv6 literal with a scope, providing the percent sign is escaped:

mongodb://[fe80::a00:27ff:fe48:af80%25eth0]

Verify whether the driver uses the scope when connecting to the server. After CDRIVER-1972, verify the driver uses the scope component if a hostname resolves to an IPv6 address with a scope component.