Eagle PCB duplicating parts
My hypothesis is that the FPGA in the schematic is drawn as multiple sub-components along the lines of U51A, U51B, U52C, etc.  U52C was intended as U51C, that's the error.  Even though there is only one sub-component of U52 present, Eagle adds the whole IC to the board.

** I've made up the designators U51 and U52.  The images in the O.P. have low resolution, and the designators aren't readable.  I'm guessing that slender vertical component on the left is the connector, and the group of components on the right is the FPGA split into multiple sub-components.