I was getting a similar error:

---
(evolution-2.8:18041): evolution-mail-WARNING **: ignored this junk plugin: not 
enabled or we have already loaded one

(evolution-2.8:18041): e-utils-WARNING **: Plugin 'Bogofilter junk plugin' 
failed to load hook 'org.gnome.evolution.mail.junk:1.0'
---

I think the spam plugins conflict with each other, so having both
enabled doesn't work (even if you don't have spamassassin installed). To
fix it, disable the spamassassin plugin. So the steps are:

1. Install bogofilter.
2. Disable the spamassassin plugin in Evolution / Edit / Plugins.
3. Restart Evolution.
4. Mark some messages as Junk (this initialises the bogofilter database).
5(?) You may need to mark one message as NOT junk before it works. I'm not sure 
about this.

Once the database ($HOME/.bogofilter/wordlist.db) has been created, you
should be able to confirm that it works by running `bogofilter` from the
command line. If it sits waiting for input, it's working.

I agree that the feedback from Evolution is poor. If spam filtering is
broken, it should at least pop up an error when clicking on the Mark As
Junk button. Otherwise the user will think that it has worked, and won't
understand why their messages aren't being filtered. Ideally it could
offer to download install bogofilter.

-- 
evolution ships with spam filtering completely mangled
https://launchpad.net/bugs/62192

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