I disagree with the opinion that disallowances u/s 40(a)(i) would be made. if the trust is registered under section 12AA and is claiming exemption u/s 11 & 12, then no disallowance can be made because calculation of income of trust is governed by sec 11, 12 & 13. Secion 28 to sec 44 does not apply to trust as there is no business income.
Only when trust defy the provisions of section 11, 12 & 13, it is possible to calculate the income of trust under business income.
However, penalty & interest for non-deduction and deposit would be applicable to trust.