Unsupported Configuration: This file is set to build for a version older than the deployment target. Functionality may be limited

Open the affected XIB files and ensure that the "Builds for" setting is set to your minimum deployment target and/or above.

Shripada's answer is correct. However, if it's still not working as Alyoshak reported, then as per this thread and my experience, you need to restart Xcode.

This was experienced with the most current version of Xcode at the time (8.3.3)

If changing the minimum build target version nor restarting does not work for you, try inspecting the XIB source file. Right click on the file → Open As → Source Code.

Look for the <dependencies> element near the top, which looks like this:

<dependencies>
    <deployment version="2304" identifier="iOS"/>
    <plugIn identifier="com.apple.InterfaceBuilder.IBCocoaTouchPlugin" version="13173"/>
    <capability name="Aspect ratio constraints" minToolsVersion="5.1"/>
    <capability name="Safe area layout guides" minToolsVersion="9.0"/>
    <capability name="documents saved in the Xcode 8 format" minToolsVersion="8.0"/>
</dependencies>

My target build was iOS 9 but the aspect ratio constraint had minToolsVersion at 5.1. When I changed it to 9.0 the warning went away.