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Questions:
1. What is the source (e.g. website, ...) from which you are attempting to download the "Kindle" books?
2. EXACTLY which application are you using to download those Kindle books?
3. "and when I tell it to use calibre instead" ?? what is the "it" you are telling to use calibre.
The macOS, for several versions now, has a component as part of the system security often called "Gatekeeper". This is sort of a firewall designed to prevent rouge applications from being run. Apple only grants "recognized developer" status to those apps sold through their Store and a few other major developers.
It is easy to get Gatekeeper to allow an independent app (e.g. calibre,...), but you need to know the "secret club handshake". Simply attempt to launch the unrecognized app, like a new installation of calibre, and when the message appears leave it on screen, access System Preferences, and select the Security section. There will be an option in the lower part of the Security panel to allow the unrecognized app. The app will then launch properly with no error or warning. You will often find that this needs to be repeated each time you upgrade the app. In my experience (up through Sierra 10.12.x) you need to do this with the main calibre app first to allow the satellite apps (Editor, ebook-viewer, ...) to function.
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