I agree with joepal. There is a "mask" modifier on the character's body mesh which is hiding some of the vertices.
Blender/Makehuman does this in order to prevent parts of the character's body protruding through the outer layers of clothing during render. You can turn the mask modifier off or delete it altogether if you want.
The way it is supposed to work is with the "add visibility" button/panel. If you turn "visibility" on, you'll get another panel in your toolbar under your MHX2 tab. You will be able to click on items in that panel to make them invisible/visible. There are drivers attached to each item and, if there is a mask modifier available for an item, it will be switched on/off as you switch visibility for a given item on/off.
Undesired appearance of the mask modifier happens for a couple of reasons:
1) You haven't activated the "visibility" function under the MHX tab.
2) You might have edited the names of items, so that they don't match the names of the mask modifier.
I suspect you are in situation #1. You are not using "visibility" and I am guessing you don't plan to. If that's the case, just go into the "Modifiers" panel for the body mesh and turn off the masking modifier. You can safely turn it off and ignore it, thereafter. If you ever decide to use it, the modifier will be available for you.
If you are using the "visibility" function, you'll have to go back and rename the mask modifiers to match the new name(s) of the clothing items you are editing. For that, we'd need to know the name(s) of the items of clothing you are using for your character and we'd need to show you where to make changes. There's a fair amount of detail in the process but it's not really hard.
If you need to know how to do that, we can certainly "fly you in" but, for now, I think you'll be all right just turning the masking modifier off and leaving it off.
If you need to know more just send up a flare.