What you were doing when the issue happenedI was trying to "Add iOS Remote" and an alert popped up in the Alfred settings pane. It says ""Alfred Remote Server needs to be running to add a new iOS Remote. Tick the "Enable Alfred Remote Server" checkbox to start Alfred Remote Server."" I notice that the message said "Tick", I wasn't sure if this was the right word for this action to fix the problem so this is why I am reporting it. Is it supposed to say "Click" instead of "Tick"?
Whether you were able to replicate it a second time by performing the same actionYes, click Remote> Un-check the "Enable Alfred Remote Server" checkbox (if Enabled)> Add iOS Remote
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Include the Alfred version & build number you are usingv3.0 
Include your OS X version