I would really need to see your drawing file to determine the specifics to the problem you are having.
However, make certain that you have selected the option "Restrict Contours to within Model Results" in the Advanced Water Surface Options dialog box. This is supposed to be on by default, but if it is off, then you will see ponding of flood water outside of the levees, etc.
Also, if there are problems with your terrain data, so that water can somehow "leak out" to these overbank areas, then you will end up with ponded water areas. This is difficult to fix unless you add additional points to the original terrain data so as to block these spots where the water can leak out.
Sincerely,
Chris E. Maeder, M.S.
Senior Technical Engineer
chris.maeder@bossintl.com