Delay in filing of ITR by Charitable Trust

Respected Sir, A charitable trust regd u/s 12A failed to file the ITR for AY 2021-22 before the due date for filing of ITR i.e. after 15/03/2022 . However it filed audit report, Form 10B before due date for filing of form 10B.  CPC  while processing u/s 143(1) has not allowed the entire expenditure as application of income and treated the gross receipts as taxable income and taxed accordingly.  In the intimation no reason given for the disallowance.  For filing appeal what grounds can be taken and  apart from appeal , any other alternative remedy available . Kindly enlighten.

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