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This is a known issue that will be fixed in future versions of this PetaLinux BSP. In future versions the PWM IP will be included in the Vivado project that is included in the BSP. These PWM IP are in the Avnet “HDL” github repository (github.com/Avnet/hdl). You can unlock get these PWM IP by rebuilding the Vivado project. The best way to do this – and modify it if desired – is to clone the git repositories and build the design using Avnet's TCL build scripts. This is described here:
Since it appears you are using Vivado 2019.2, just be sure to checkout the 2019.2 branch instead of the 2019.1 branch.