The basic reason for this error is non-processing of data by GSTN’s server. As soon as the taxpayer fills up the data in Eligible ITC and clicks on save, the data takes some time to reflect as ITC. If in between we proceed for payment of tax liability, the system will not reflect the input tax credit amount that we need to claim and thus will adjust the old input tax credit with GST liability.
The most simple way to overcome this situation is to wait for 5 minutes once Save GSTR-3B is done. The amount will reflect as saved when you refresh the screen and now when you proceed with return filing, your input tax credit will reflect as submitted.