@Jon The only possible scenario for which you have observed the issue, I could think about would be when you are using HTTP Trigger logic app workflow.
When your logic app workflow doesn't handle the endpoint validation with HTTP trigger. When you create the event grid subscription then to prove endpoint ownership the endpoint needs to echo back the validation code in the validationResponse property as mentioned in the endpoint validation document.
Once you create the event grid subscription it waits for a few minutes for the validation response and till that time you will see an event grid subscription under your topics.
In case if you are not able to validate the ownership of the endpoint within the time limit the event grid subscription will automatically be deleted as you were not able to validate the ownership of the endpoint.
The above could be one of the reasons but if someone is still facing the issue then please share the details as requested in my comment to assist you further.