This is a bit roundabout, but you *can* delete specific entries from
your cert DB. This involves messing around with the command line a bit,
and is far more involved than it should be. That said, the following
worked for me.

Close Epiphany, then open
~/.gnome2/epiphany/mozilla/epiphany/cert_override.txt in a text editor,
and you should see something like the following:

---
# PSM Certificate Override Settings file
# This is a generated file!  Do not edit.
bugs.freedesktop.org:443        OID.2.16.840.1.101.3.4.2.1      
58:43:9C:2D:39:61:1C:53:67:1D:A0:DB:08:06:C4:36:74:A2:7E:34:B5:08:51:9E:ED:73:CB:D7:D5:2C:89:AD
 U       AAAAAAAAAAAAAAADAAAAewYRmTB5MRAwDgYDVQQKEwdSb290IENBMR4wHAYDVQQL  
ExVodHRwOi8vd3d3LmNhY2VydC5vcmcxIjAgBgNVBAMTGUNBIENlcnQgU2lnbmlu  
ZyBBdXRob3JpdHkxITAfBgkqhkiG9w0BCQEWEnN1cHBvcnRAY2FjZXJ0Lm9yZw==
---

(Everything from "bugs.freedesktop.org" to the last "==" is one very
long line.) Delete the line(s) corresponding to the certificate(s) you
want to delete, and restart Epiphany. The certificate exception should
be revoked, and you should see the same warning when you go to the
relevant page that you did before you added the exception.

Please let me know if if this does or does not work for you.

** Changed in: epiphany-browser (Ubuntu)
       Status: New => Confirmed

-- 
Certificate manager can't delete certificate exception.
https://bugs.launchpad.net/bugs/314859
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