please specify for which month as from the month of April GSTR1 is being filed before GSTR3B. the excess amount will credited in your credit Ledger and you will have to adjust the same in the next month return.
No adjustment of taxes is currently available if there is difference in 3B and GSTR1. File your GSTR 1 with correct value first.Then reduce your liability in 3B in next month return by the excess amount paid in june.
If you consider an invoice a higher amount then you have to issue credit note of such excess amount and in the next month the turnover and the tax will be decrease by such excess tax paid on excess turnover. This is the only way you can reverse this, you cant get the refund for excess amount after set off liability.