The SQLServer in combination with the JDBC driver does not take care about upper and lower cases for names, but the Dynatrace server does. If an application is using the same name, only distinguishable by an upper/lower case letter, the mentioned exception will be triggered by the database. This is because a measure with the upper case writing and a measure with lower case writing should be inserted into the dynamic_measure table. If the DB-system cannot distinguish between upper and lower case writing, an already inserted measure definition should be inserted again.
The same application name with different case can be caused either by a manual setup or by the application auto detection.