This will occur when you hit build or clean sometimes if you have a relative path set in your project for your temporary directory (for me it occurs most frequently after an upgrade to a new SDK).
To fix this issue (which is an internal XCode compiler issue) smply add $(PROJECT_DIR) as the root for CONFIGURATION_TEMP_DIR and then Xcode will cooperate again.
iPhone/Xcode - "error while creating dependancy graph"
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