gene duplicated on genome but is different
That sounds line one of two things. Either a sequencing or assembly error (quite likely since you're talking about scaffolds so, presumably, not a completely assembled genome) or duplication and subsequent pseudogenization. 

It is relatively common for genes to be duplicated and then to be rendered inactive by a mutation event. Such genes can still be detected in the genome and are called pseudogenes. The process of their creation is, unsurprisingly, called pseudogenization. You can think of such genes as fossils. They often have significant sequence similarity to the original and can even be transcribed. 

A quick search brought up a couple of articles discussing the pseudogenization of specific genes:


Pseudogenization of CCL14 in the Ochotonidae (pika) family.
Pseudogenization of sopA and sopE2 is functionally linked and contributes to virulence of Salmonella enterica serovar Typhi.


That said, is also quite possible that what you describe is a simple duplicate that has diverged without becoming a pseudogene. The details will depend on the particular sequence. Are there in-frame STOP codons? Can the gene still be transcribed? Such duplication events give rise to paralogs (note that all three of the genes you mention would be paralogs of each other, it's just that one has diverged more than the others). You can read more about those here: What is the difference between orthologs, paralogs and homologs?