Had the same issue; after installing latest patchest for Linux as of today the issue persisted, so I fixed my savegame like this:
http://pastebin.com/m4gGePNm
You'll need a working Python interpreter (most Linux distros do) or do the fix youself using a hexeditor.
1) Unzip savegame
2) Make a copy
3) Run script
4) Zip the savegame and replace in the game
Remember about backups, and best - do it after resting so it won't reenable something it should - to keep the game fair.
# Fix Pillars of Eternity save game with locked 1 per Encounter ability (In my case Grimoire Slam)
# mkdir save
# cd save
# unzip ../*.savegame # unzip only one you want to fix
# cp MobileObjects.save MobileObjects.save_ORIG
# Run in python interpreter:
import re
data = open('MobileObjects.save_ORIG').read()
# Fix / patch (selected as the most common in my savegame)
good='m_activated\x06\x01\x11\x01\x06\x01\x00\x06\x01'
# Pattern to find and fix (only 1 occurence in my savegame)
pattern='m_activated\x06\x01\x11\x01' + '\x06\x01\x01\x06\x01'
fixed = re.sub(pattern, good, data)
f = open('MobileObjects.save', 'w')
f.write(fixed)
f.close()
# zip -r 'savegamename.savegame' *
# cp savegamename.savegame ..
# Try loading