Some of the scenes appear to have fog enabled and / or lightmapping data. Please modify "Shader stripping" settings to always include required shader variants.
Depending on the exact project structure, Unity might consider fog and / or lightmapping shader variants as not required and strip them from available shader variants. Unfortunately, there is no way to force-include those variants via Editor API, thus Luna has to instruct developers to mark such variants as always included into the build via Unity Graphics settings.
Medium / High
Please navigate to "Shader Stripping" section in "Graphics" section of project settings and enable lightmap and fog modes used by your scenes: