The crew elects to do a GPS approach onto RW18. It is a long evening and both crew members are tired, so instead of using the GPS approach charts take out the LOC charts for RW18 by mistake.
I would imagine that if the LOC/DME was in service they would have been shooting that approach (we'll know soon enough what approach they were cleared for). As is depicted on the chart, at runway threshold the DME reads 1.3 (to the far end, like SFO 28L). If they thought they were farther from the field than they were, they would have been high, not low.