this is in three different data bases

We have inventory items that show no cost but a quantity on hand.
We have inventory items that show cost but no quantity on hand.
Some items on our drop down screen of inventory costing have lot 1 with negative inventory & cost.
Lot 2 shows receipt & positive quantity & inventory. The average cost shows as lot 2 divided by on hand amount less the cost of lot one. Lot 2 will not move up.
We have work arounds to fix most of these by making adjustments but my concern is the cause. How do we stop this happening on what appears to be a totally random basis.
Is there an easy fix or do we adjust our heads off?