This is common with all QC versions.
Sometimes, a project will not ''delete'' for various reasons.
When you perform a ''delete'' from Site Administrator, what it does is 3 things:
1) Deletes the Repository folder corresponding to the project,
2) Deletes the database/Schema relating to the project, and
3) Deletes the RECORD corresponding to the project from the ''PROJECTS'' table in the qcsiteadmin_db Schema/Database.
You can do all 3 steps MANUALLY if you want.
Of course, BE VERY CAREFUL that you delete the correct folder/record/Schema.
It might take a cycle of the QC/ALM Service to see that the project is out of the list.