From your vague description of the issue you have, I think it may be the same problem as described in this thread...but at a different point in the model:
viewtopic.php?f=9&t=3677
If it is, temporarily modifying your layer height by a very small amount....for example from 0.2mm to 0.2001mm.....may cure the problem. If it does, then running the model through the Netfabb repair tool (link in the above thread) will probably cure it permanently.
If the issue is not this, then you need to post your factory file as requested above so as to give someone a chance to see what is wrong.