GetSingleton<T>() requires that exactly one entity exist that match this query, but there are 0.

Removed all GetSingleton calls and still get this message.

Solution. In my test initializer I had code that cleans up all the entities before test to avoid situation where Unity creates n amount of entities that might change. Well this complicates things, but is solved.

This can be the case when you destroy singletons used by systems that assume they will be present after the system creates them, usually in OnCreate. It seems like it’s considered an error to perform destructive actions on singletons, so arbitrary catch-all entity destructions should be avoided. The singleton in question here (PhysicsAnalyticsSingleton) is such a singleton (created by BuildPhysicsWorld).
Similar example:
https://discussions.unity.com/t/878960

I have personally also get this sometimes. However, other than what was written above, reimport all has also helped me when I could not find any code-related problems.