Question: Why one gene can be present more than once in annotation?

[ne1al]

Hello, I used prokka to annotate draft asssemblies followed by Roary for presence/absence matrix. Interestingly, I find the same gene sometimes or same gene_number (geneX_1,geneX_2) with different abundancies! One time it shows in all the draft assemblies, another time it shows in only a proportion of it. Could you kindly advise?