We have an application that is not showing on our list. Applicant has acknowledgment but we can not see application on the JOTform site

I am not sure if I understand your query correctly. Do you mean to say that you are receiving a notification email but the form is in your JotForm account? Could you let us know the email address that you have received the notification and a screenshot of the email so that we can try locating the form for you? 

Let us know if you are referring something different. We will be happy to help. 

Sorry. I mean to ask if the form is not in your JotForm account.