There are already multiple workarounds posted for this issue. And in this comment, I will try to provide the underlying issue why this may be failing. [With the hope to make people aware of the root cause]
Let's say, you have a DbContext (to be specific, child class of DbContext) in your application, and you are trying to use a model class (let's say Model) and the DbContext and scaffolding controllers / views.
I am guessing that the DbContext did not have a "DbSet< Model > Models {get; set;}" property on it but the DbSet was nevertheless added to the DbContext using code in OnModelCreating method.
In the above case, scaffolding first tries to detect DbSet property on DbContext (by reflection only - so that does not detect if OnModelCreating has code to add the DbSet) and given it's not, scaffolding adds a DbSet property to the DbContext and then tries to scaffold using that DbContext , however when running the scaffolding, we create an instance of DbContext and we also call OnModelCreating , and at that point, scaffolding fails because there are multiple DbSet types with the same model in the DbContext (one added by scaffolding and one configured in code in OnModelCreating).
[This happens not only for the model being used but also for related models in that model , scaffolding adds DbSet properties for all related models]
[Also, one doesn't see the added DbSet's after the scaffolding is done because scaffolding rolls back any changes if the operation did not complete successfully, like Jeff mentioned , the error message was poor initially and was improved to give some hint to the user but it's still not super clear what's going on]
This is a bug in scaffolding , a simple work around would be to use DbSet property on DbContext for all related models of your model class instead of configuring them in OnModelCreating.