Depreciation Calculation Fails with Unique constraint error when run in bulk

When we run the Depreciation calculations for pending open transactions as a whole (At a business unit level). But if the same set of assets are run individually (by inserting assets into the run control record), the process calculates the depreciation for all assets and goes to success. We are wondering whether there is a way to restrict the program to calculate the number of assets. Strangely we have had  (in the past instances ) where we processed more assets in bulk.

Thanks in advance.