Transactions with fee amount don't show up properly in batches
The current batch total in CiviCRM is confusing as it is summing the amounts for all of the bookkeeping entries in the batch, NOT the total payments received for the contributions included or the total expected revenue from them. 

To see this clearly, if you edit a contribution and change most fields this results in reversing and reposting a corrected copy of the transaction. Putting all of the relevant bookkeeping transactions into a batch results in a 'batch total' significantly larger than the contribution, even if you haven't changed the contribution amount.

We're finalizing (Sep 2017) some new functionality in core and extensions that will allow some batches to be used to more easily track batches of payments, and other ones to deal with non-payment bookkeeping entries.