The most common cause for this issue is the setup for the letter templates within Workflow Maintenance.
In order to resolve this follow the below steps:
Open Workflow Maintenance
Select the correct case type and find the template which is going in the wrong folder
Click Update at the bottom of the screen and on the left hand side locate the option called folder. There is also an option for Update Multiple in case more than just one template requires updating
Select the folder you want the template to be automatically assigned too
Save and Exit
If you do not have access to Workflow Maintenance or struggle with the above instructions please raise a new case online and reference the title of this article.