After lodging batches of tax returns if some returns have been rejected you should:
Check the reason for the ATO rejecting the return(s)
If an SBR error, select the Client, Tax Return, check for Errors and resolve
Once the form is free of errors, relodge the Tax Return
NOTE: IF you are receiving EM errors please refer to the article Error on lodgment that starts with EM
If the issue persists please raise a case online , attaching the HandiTax data, include the PDF of the lodgement report and attaching screenshots so it can be investigated for you.