did you recently change the settings (Project → Settings → runtime) where the uniqueness is calculated?
Or did you recently upgrade the project to mx9?
In the past Mendix gave you the option to choose where the uniqueness was being set, runtime or in the database. From (I believe) Mendix 9, this is always in database. Mendix developed the MigrationToolkit to help you remove the duplicate values and enable the “database” variant of the uniqueness validation.
Have a look at:
You can contact Mx support for the toolkit.