Same issue in UE 5.5 (and 5.4) too. I don’t even need to add anything to the project, just enabling the Water plugins breaks the packaging. There are 6 similar error messages:
UATHelper: Packaging (Windows): LogInit: Display: LogCook: Error: Content is missing from cook. Source package referenced an object in target package but the target package was marked NeverCook or is not cookable for the target platform.
UATHelper: Packaging (Windows): Source package: /Landmass/Landscape/BlueprintBrushes/Materials/Sprite/M_BrushSprite_01
UATHelper: Packaging (Windows): Target package: /Engine/EditorResources/S_Terrain
UATHelper: Packaging (Windows): Referenced object: /Engine/EditorResources/S_Terrain.S_Terrain
The workaround is (from here):
Project Settings → Packaging → Advanced → Uncheck “Exclude editor content when cooking”
Not sure yet of the consequences but at least packaging works and my build plays as expected.
But I am really not sure about using the Water plugin in a release now.