This warning message is not usually a concern. It is just saying that the number of elements force cards that could be found in the F06 file is less than those that were read in from the finite element model. In some cases, if you have CROD elements in your model, the count of element forces found in the *.F06 file will report that it is less than in the imported FEM. This warning message is inaccurate and will be corrected in Version 5.4.
This message was originally intended to warn you if the *.F06 file did not match the *.DAT file. As long as you are sure that the F06 file and nastran bulk data file match each other, you can safely ignore this message.