Question about API Keys

I was using the same API key and encryption key for uplink and filezilla. I uploaded a file in filezilla, but that file could not be seen when using uplink and the other way around.

Shouldn’t that have been the case?

This will be case if you use different accounts or projects. There is no other way to have such an issue.
Any API key (Access grant) for the same project will give you an access to your buckets and data. However, you also need to have the same encryption phrase, otherwise you will see only empty buckets.