That's because dpkg refuses to replace a directory by a symlink on upgrade. 
This upload fixes the issue:

 epiphany-browser (2.14.1-0ubuntu2) dapper; urgency=low
 .
   * debian/epiphany-browser.postinst:
     - fix symlink creation on upgrade (Ubuntu: #38953)
   * debian/control.in, debian/rules:
     - build the html API, upstream didn't ship it with the tarball

** Changed in: epiphany-browser (Ubuntu)
       Status: Unconfirmed => Fix Released
-- 
Cannot access help within Epiphany
https://launchpad.net/malone/bugs/38953

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