Generally Day One 2.0 does not have issues with duplicate entries. Duplicate entries appear sometimes from importing duplicate data from Day One Classic (version 1).
Since the entries in version 2.0 will have a unique entry ID, there is not an automatic way to resolve these at this time.
The best way to resolve duplicate entries in version 2.0 is to manually delete them. This can be accomplished fairly quickly by using the Multi-Select Tool in Day One for iOS. This allows you to quickly select multiple entries and delete them all at once.
In Day One for macOS, you can use Command-click on multiple entries to select them. Right-click on a selected entry and choose Delete.