Journals would normally be T9 so shouldn't hit the VAT return at all.  A little more detail on the problem would be helpful. Are you on on the VAT cash accounting scheme or standard accounts?  Can you give an example of the items that are appearing in box 6 that shouldn't? 

There are situations where a supplier refund appears as sales income and customer refunds appear as expenditure.  Is that the kind of thing you are referring to?  If so, that can be adjusted but can you say a bit more first?