Yes and no. If the fill is full of junk like tree stumps or if the fill is not compacted properly, yes, you can have settling and the house may sink unevenly. Fill can (and often should) be laid down in layers, with each layer being compacted by a heavy machine designed for the task. Do the construction plans call for compaction of the fill? Do you have an engineer to inspect the work as it progresses? You need a solid base to build the foundation on.