If a file has been created in SNAP (for example spatial subset) but not saved on disk, it appears in the product view. The reader in Graph builder accepts any filename that appears in Product View as an input image. If such non-saved product is used in a Graph as an input file everything proceeds without an error, but when the output of the graph is inspected it turns out that some other input file had been used. A workaround for this problem is to 1st save the input product on disk and then running the graph.
This issues is related to issue SNAP-171, which should be lifted to priority major.