It can be tricky to delete an external. This is kind of on purpose. 
You see, you may have some files out there somewhere that are still using these things – in which case??? What would happen?
So…
Partials, Templates, and Externals have some fail-safe features built in. This can be a bit frustrating if you’re really trying to get them to go away.
Failsafe #1: You can’t delete them from inside RapidWeaver.
- reason: early users were were deleting Externals in one file that they had used in another file – not realizing the consequence. so i took away the ability to delete them perminently.
- workaround: quit RW. open your add-ons folder. move the external to the trash.
Failsafe #2: Every project that uses an External/Template has a fail-safe copy of that External/Template inside. So, even if you do move something to the trash, it will still come back to life if you’re using it somewhere.
- reason: this is mostly so that you can send a friend/colleague your RW file without sending the externals/templates too. when the friend opens the file all the externals just behave like partials.
- workaround: to really get an external to go away you’ll need to completely stop using it.
Failsafe #3: When you try to edit things that should have a file – they’ll make a file
- reason: everyone wants to edit their templates eventually. when you try to edit a template it will ask if you’d like to make an external or partial from it instead. if you had previously deleted this file it may resurrect the file inside the addons folder in order to write your changes.
- workaround: if you don’t want your change written to a file, use a partial instead. they don’t write to a file.
Even with all those failsafes, all this kevlar bullet-proofing, there are still ways for users to shoot their own toes off. 
Here is a fun exercise for the pro users out there:
An external that references images keeps a copy of those images inside of itself. But, if you’re very careful, there is at least one very well hidden way to thread the needle of all the protections and manage to delete all of the copies of the referenced image – yet maintain a multiple-time-reanimated copy of a an external that no longer has the images in tact.
This requires that you physically move the external to the trash no fewer than twice – and ALSO – delete all of the copies of this image within the RapidWeaver resources – and THEN – somehow (left as an exercise to the reader) keep using this external in another document.
LOL.
Needless to say, there are a lot of protections. They are there on purpose. And deleting these things is (intentionally!!!) very difficult.
Not every surprising behavior is a bug. 
Sometimes those things are there because I’m looking out for you guys. 
That said, if you do find a bug, please let us know. Here is a link to the bug tracker please feel free to have a look or add your own (you’ll have to sign in – just to prevent spammers).