Stacey, there are a number of ways to fix that. What I would use, and recommend, is a cement-based patching compound. Armstrong puts out a good one, called S-184 Fast Setting Patch. But there are other brands (Ardex, Henry's, etc) equally as good and like Armstrong's product, available in small 5 to 10 lb. boxes. Found most anywhere flooring products are sold, including Home Depot and Lowes. Mapei make a good one too but you don't need a 50 lb. pail of it.
When you apply the patch, make sure you have enough pea gravel over the exposed liner so you don't create a dam. In other words, take the patching compound down to the pea gravel, but not all the way down to the liner, keep a pathway open to the weep holes. Expect that to set up in 1 hour or less.