Yes, follow this tutorial to add a navmesh tonyour map.
https://developer.valvesoftware.com/wiki/Half-Life:_Alyx_Workshop_Tools/Level_Design/Navigation_Mesh

Ungol mentioned ai_nodes below. Does that cover the frozen enemies like the zombies and antlions?

nav mesh fixes the headcrabs being black and staying hopping around without a animation but its only for headcrabs that it fixes it

Just watched a bit of Skummeh's playthrrough. Looks like ya don't have a nav mesh.

Also the hands being black in the start means the env_combined_light_probe_volume/cubemaps are incorrect.

The layout as visual assets used are great but the enemies are broken among other issues. Also I somehow missed your comment about the multitool so I went searching for it but not for long. Detailed feedback video here: https://youtu.be/F3IncNKvIhI

Do you when you'll have time to add that to the game? looks great wish I could of kept going.

there's no ai nodes, the lighting at spawn is a bit broke, making your hands and guns all black, and the explosive barrels at the 3 zombies is a dynamic prop, meaning it can't be blown up, the square green bottle next to the vodka is also a dynamic prop, the hazmat worker has broken lighting on their mask and they're tinted green. overall it's still a great setting.

Before anybody says it, I know that i forgot to give the multitool to the player. Im going to fix that