My sister and brother and law filed married filing jointly but they chose the refund to be deposited into her account which is under her name will the refund be rejected

She should ask her bank.... The bank might accept it....or not...if the bank refuses it because both names are not on the account then it will go back to the IRS.  Then the IRS will have to mail them a check.

No if they filed a joint return, and the bank information is correct the IRS will deposit the refund into your sister's account.

You are allowed to split your refund into several accounts.  I wouldn't expect only one name on the account would make a difference.  As long as she is one of the names on the return that's filed you shouldn't have a problem.