The reason that happened in my case was some developer updated a pod A while I installed a new pod B (without updated pod A). So when I merged his codes I got the warning.
An easy way to fix this is to
1. remove libPods.a from General->Linked Frameworks and libraries
2. run `pod install` or `pod update "an-existing-pod"` again.
For step #2 the purpose is to update .xcodeproj file not to install pod again. If pod is already there cocoapods will just update .xcodeproj file.