Hello Vagelis Kretsimos,
As you might already know, this error usually appears when there are two or more controls in the page with same ID. In Sitefinity it can be reproduced in multiple ways. For example, if you try to add controls with same ID in the master page and in the Sitefinity page under same container. Or if you add such controls in a template and a page again in same container.
Unfortunately, we are not able to reproduce your situation. Could you give us steps on how to get the error? You said that it does not show always but it would be very helpful to tell us how we could reproduce it. Thanks in advance.
the Telerik team