My client is on Dynamics CRM 2013 SP1 UR1 and they are facing this problem for their multi-org on-premise deployment. They have a pretty simple workflow on the account entity where they are sending an e-mail and in the e-mail body they are inserting a hyperlink to the account record.
The problem is that when the user is clicking the record URL in the e-mail, since it does not contain the Organization name, it is redirecting to the default organization. Since that organization does not have the record existing, it is giving an error to the end-user.
The issue would be addressed by Microsoft in the Update Rollup 2 of SP1. This can be found in the Fixed Issue section of the download page for the update rollup.
Hope this helps!