Today I had such strange warning when compiling cocos2d project in XCode:
Warning: Multiple build commands for output file
And result was even stranger – for even builds everything was ok, for odd one of sprites had much bigger size then it should. The reason was simple, but hard to find – I had 2 files with same name in my resources folder, one in root, one in subfolders. First was small so it displayed as it should, second had different purpose so it was much bigger. So the wrong sprite size happened when xcode used second sprite. Solution is simple – just had to rename one of files, and keep track of their names to avoid such situations in future.