Depending on the match criteria you use for assembly, it may be possible for reads from two or more homologous regions to assemble together, though in most cases distinct flanking sequence regions from the different homologs should prevent this. More likely, distinct alleles of the same gene may be assembled into the same position of a contig due to their very close sequence similarity—this is typically what you would want to happen. However, you may select Contig > Split as Suggested to split contigs to resolve constituent reads into contigs for distinct homologs or distinct alleles/variant haplotypes.