Can someone explain this behavior?

Buffer.from('5d9RAjZ2GCob-86_Ql', 'base64url').toString('base64url')

// 5d9RAjZ2GCob-86_Qg

Please take a close look at the last character l - g

>Solution :

Your string is 18 characters long, With 6 Bits encoded in each character it means the first 16 characters represent 96 bytes and the last two represent one byte plus 4 unused bits. Only the first two bits of the last character are significant here. g is 100000, l is 100101. As the last 4 characters are not used, g is just the first choice for the two bits 1 0.

So for any character in the range between g and v, you would get a g when you convert it back to Base64Url.
See https://en.wikipedia.org/wiki/Base64#Base64_table_from_RFC_4648