In the C. elegans chromosome X (NC_003284.9) is a complete copy of the C. elegans fosmid H05L03 (FO081428.1) at positions 5898291-5912640. I understand fosmids are vectors used to build sequencing libraries, so is this a contamination?
The chromsome X sequence was assembled from genomic DNA fragments that were packaged into fosmids. In this case, your fosmid (FO081428.1) was one of a number of fosmids that were assembled together to form the inferred chromosome X sequence (NC_003284.9). So this is not a contamination - in fact the chr X sequence was literally assembled from many individual fosmid insert sequences. See the contig entry in the chr X genbank record here.