Ok, I've found a way to fix this problem. Here's a step-by-step guide. Feel free to redirect anybody with a similar problem to this post maybe it will save them a lot of aggravation!! It's a longwinded guide but I've tried to keep a lot of detail so a zbrush beginner could follow it.
1. Go to the subdiv level at which the problem is apparent. (usually highest)
2. Press Delete which zooms the view out to encompass the whole model. The main model will be on one side and the naughty polys on the other.
3. Ctrl+drag a masque around your model. This will allow you to move the polys into place without affecting the rest of the model.
4. Select the move tool and adjust the size to about 150. Wave it around the edges of the document until it highlights the polys. Drag the polys towards the model. This will probably have to be done in several moves, gradually shoving the polys home.
5. When you have dragged them near the model, press delete to resize the view. If the view zooms in filling the frame with your model the polys are in the right general place, at least from this angle.
6. Rotate and press delete a few times to chek that the polys are near the main model in 3d Space. If the view zooms out as before with model on one edge of the frame- repeat previous steps.
7. Select Smooth tool max out the size and strength and smooth over the whole frame. This will only move the polys bak to their home...everything else should still be masked off.
8. Remove sections of the mesh surface (ctrl+shift+drag) if the polys have moved somewhere inside the model. Switch local on, this will allow you to rotate the model around the polys. Even if you can't actually see them you will know where they are as they will now be at the centre of the rotation. Keep using the smooth brush over this point until the polys move to their old home on the mesh surface.
9. That should be it! If you inspect the surface of the model you should see a grey spot showing up against the black(masked off) model. When you are happy clear the mask.
Hope that helps. Now I can finish the model. I'll post a link here to it when it's done!