How to reproduce:

1. Create a host and link a template with LLD rule to it (e.g. Template OS Linux)
2. Update an item prototype - assign an application prototype to it (e.g. {#FSNAME})
3. Wait until Zabbix will add items and applications
4. Update item prototype in the template and set "Application prototypes: None"
5. The items created by LLD remain on the host with "flags: 4" (but must be deleted)
6. Try to delete created application from the host. Web interface generates error:

   Cannot delete application
   
   Cannot delete discovered application "/boot". [applications.php:188 ? CFrontendApiWrapper->delete() ? CApiWrapper->__call() ? CFrontendApiWrapper->callMethod() ? CApiWrapper->callMethod() ? CFrontendApiWrapper->callClientMethod() ? CLocalApiClient->callMethod() ? call_user_func_array() ? CApplication->delete() ? CApiService::exception() in include/classes/api/services/CApplication.php:417]

You will not be able to reproduce this issue if will perform step No. 4 on the host (instead of the template).