When 200 MHz and 50 MHz are generated from a 100 MHz clock source, Clock Generator will use two DCM's instead of one DCM.
This problem has been fixed in the latest EDK 10.1 Service Pack, available at:
http://www.xilinx.com/xlnx/xil_sw_updates_home.jsp
The first service pack containing the fix is EDK 10.1 Service Pack 1.