After the patch, when I’m in my WoD garrison, the Call to Arms button appears.
Previously, I put the Call to Arms ability in Action Bar 5 and then just hid Action Bar 5. After the patch, if Action Bar 5 is hidden, the Call to Arms button reappears in the lower center area of my screen.
The Call to Arms button now appears both inside the WoD garrison and in other WoD zones. Placing Call to Arms on an Action Bar does not remove the Call to Arms button. This appears to be a new bug. Please fix.
I had this issue too. I discovered if I went into Options/Action Bars and ticked Action Bar 4 (where I have my Call to Arms button) it would then hide the Call to Arms button on the screen and only show it on Action Bar 4.
So, whichever bar you place your Call to Arms button should be ticked in Options/Action Bars.
I use Bartender but tested this without it enabled and it still works. If you are using Bartender you can then hide the Action Bar with the Call to Arms button on it and it will be hidden.
Worth a shot if it works 
Unfortunately, I don’t use Bartender.
With all the LUA errors between addons and WoW after patch 10.0.5, I’m trying to minimize the number of addons that I use.
I just tested without Bartender enabled and was able to still hide the Action Bar via “Edit Mode”.
As long as I had that bar checked with a tick in the Options/Action Bars section the Call to Arms button would stay on the bar but be hidden.
That worked! Thanks!