Hey micperk - the first big flaw people make is with their rivers.
There's loads to be said about rivers and many here will tell you all about that.
As rivers flow down from their source, they don't split apart with the exception of a river delta or a man-made feature like a canal.
Many writers make this mistake and it is by far the biggest. Even fantasy reasons don't usually explain it away either.
There are other things like really unlikely mixes of terrain and biome features that wouldn't exist together normally.

There are also things that get done far too often but those are not really wrong, just somewhat tired.
Best thing to do is rough sketch a map and ask for suggestions of what might be wrong.
If you are trying to keep it hush hush then you can private message some particular users for their advice.
[Though you have to have more than 5 posts before you can use the private message system.]

There are various members who have much more knowledge in certain areas who could be of a lot of help.
Pixie and Azelor discuss plate tectonics and climate a lot and are quite knowledgeable there.
Chick knows a lot about geology and various other things.
The HoarseWhisperer and various others know quite a lot about certain time periods and city layouts and such.
There's a host of various expert info here. Just ask more specific questions to get better advice.
Cheers,
John