Considering that your label this question as RNA Seq, I suppose you are talking about RNA Seq data. To understand why the reads should be mapped on the same contig, you need to understand how we construct the RNA Sequencing data. If you read this you can see that our original materials are the RNA transcript. Therefore the fragments we used to build the reads will be originated from the same transcript. However, if there are fusion genes within your data, the transcript might be originated from two different genes, therefore your resulting RNA Seq pair end reads can map to different genes.