Take a look at this. You see the area in the middle. For some reason when I apply bevel on it. It gets really nasty, any ideas why this is?
Looks like you may have some inverted normals.
This seems to be a common thing when using Blender curves to generate meshes.
Select the mesh in Edit mode and hit “CTRL+N” to recalculate the normals and try again.
No that is not it. As you can see in the wire it’s all messed up when the two arms meet. I would like if possible just the bevel to happen where the edges are. Like if you would bevel letters in photoshop.
do you have two bevel modifiers on it?
The only way I’m getting similar results is by doing that, even when applied that does weird things because it seems the first one makes odd faces in places, messing up the second one completely.
Here is the blend, please take a look because I have no idea what is wrong with the mesh.
Attachments
sf.blend (294 KB)
I’d be able to give better feedback if I knew what you were trying to make it look like.
What version of blender are you useing? if it’s 2.4X you can use the selective edge bevel tool, that will do a much better job, just a bit slower, but for the amount of work you have that wont be to hard.
To my knowledge the bevel modifier’s in 2.5 are all ether missing, or only partially working. so not much hope there but to wait or help out yourself.
the base mesh itself looks great though, honestly I don’t see that you need to do much more to it.
Under scripts there is the bevel center ( oh if your in 2.49 ) IT will ignore inside corners.
- decrease the bevel width (I think 0.25 looks pretty good)
- limit the bevel by angle and set angle to something like 65° to limit which edges get beveled
It will still have issues as apparently the bevel modifier doesn’t like verts with >4 edges (aka “poles”), but it looks a bit better that way. 
Use edge loops instead of bevel. At this time, bevel in blender is horrid. No NGons support.
There are a bevel add-on for manage bevel edges and influence.
Video tutorial and the link to the add-on: