I would start by looking at how your inventory component parts on the BOM are classified.  I have had production put an item I deemed as N- Non Inventory and classified as such in a BOM then they changed it to a P-Purchased Part. Or vice versa a P changed to an N but not taken of the BOM. The timing is important here because if they changed it half way thru production not at the beginning.  If that is the case be sure to look at your COGS as well to make sure exactly where it is being expensed to.  In order to fix I believe (its been awhile since I had to fix this issue) you need to correct the N or P issue, check the correct pricing, check the BOM (I can't remember if I did a rollup on this before the next step or not), and then run WO-K-H to Rebuild the work order costs.  I also limited who has access to the IN-E after that.  Haven't had a problem since.

The cost in JC-E is showing negative cost. How do I fix that.

I'm not sure if that what happened but what can I do to fix this? The material is negative and on some of them there is not even any material showing it was issued to the job on the workorder.