this folder is probably not empty.
There may be some hidden files (files starting with .) left there.
ls -la /home/<username>
To find it out.
You may also use
to remove a non empty directory and all its content
to force the removal without displaying any messages.
How did you remove the user?
If you used userdel the -r option would have removed the homedirectory of the user:
userdel - Delete a user account and related files
userdel [-r] login
The userdel command modifies the system account files, deleting all
entries that refer to login. The named user must exist. The options
which apply to the userdel command are:
-r Files in the user's home directory will be removed along with the
home directory itself and the user's mail spool. Files located in
other file systems will have to be searched for and deleted manu-