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Under investigation by the game team
If you have completed all Guild Tasks for a particular color you should receive a bonus. Sometimes, this stat bonus is not being displayed and it may appear as if you aren't receiving the bonus. They may also appear incorrect on the Team Bonuses.
Fixing the problem
This is a display issue only. The Gems of War team has investigated and discovered that the bonuses are correctly applying.
To check, open Troops > Crafting menu > Skills tab, and look for the "+X for Guild Bonus" which you should have.