I checked from other sources and seems that I'm wrong and that previous years also the amount was 5% of Gross income and not 10%, somehow the limit was hit in this years filing and that's why the confusion.

I'm extremely sorry for this wrong comment earlier.  I cannot find a way to delete the previous comment.

ALL Kindly DISREGARD my previous comment. 80G deduction in 50% of Donation with qualifying limit gives effective deduction in taxable income by only 5% of gross income. 
It happens as a rare event that the qualifying limit is hit, and then a wrong interpretation can cause some misunderstandings.

Sameer Bahadur sir.

For AY 2021-2022, I found that 50% of the actual donation I had paid (eligible u/s 80G) was less than 10% of the AGTI, but more than 5% of the AGTI. The System thus allowed a 80G deduction in Schedule VI to the extent of 50% of the amount paid as donation for AY 2021-22. From this, it is clear that till AY 2021-22, the maximum deduction amount that could be claimed u/s 80G was lower of (i) 50% of the amount paid as donation (eligible u/s 80G) and (ii) 10% of the AGTI.

I am not aware of any amendment made thereafter. If anyone has any information on this, please do post it. Thanks.

I feel the Department should have a re-look at their interpretation of the ceiling of 5% incorporated in their system that calculates 80G deduction for AY 2023-24, and restore it to 10%.

Since I did not hit the cap last year I do cannot confirm on the dynamics of the ITR forms.
There is one thing you might check -
AGTI that is shown in the IT Return calculation (ie the amount after all deductions, on which tax is calculated) is not the 'Income Value' used for 80G calculation.
Income Value calculation for 80G - has all Schedule VI entries deduction but not the 80G entry itself. So if by chance you calculated AGTI wilh all Sch VI deductions (including 80G) you will have a slightly smaller AGTI, when compared to the Income Value where 80G deduction amount is not deducted from income. 

So with this slightly smaller AGTI you may calculate and find your 80G deduction amount to be slightly higher than 5%, but might actually be less than the (AGTI+80G)*5% limit hence not trimmed, and you would see the whole 80G acceptable as eligible that year

Sameer Bahadur sir,

Thanks for your prompt response. Yes, I had calculated AGTI according to the rules: From total gross income, excluded all capital gains, exempt income, all deductions claimed in Schedule VI (other than 80G). On the resulting figure of AGTI, in AY 2021-22, the system automatically compared 50% of the listed 80G donation amounts, and thereafter filled in the permitted 80G deduction amount in Schedule VI. As mentioned by me earlier, this 80G allowance happened to be exactly 50% of my gross 80G donation figure. The deduction was more than 5%  but less than 10% of the AGTI, which leads me to the conclusion that the ceiling of 5% incorporated in the AY 2023-24 software needs a re-look, on the presumption that there has been no change in the rules since AY2021-22.

I also ran into the same issue. I can only claim upto 5% of ATGI instead of 10% ATGI. What to do now ?

Replying to Suresh Mollyn sir.

I would request you to please check, if in any previous AY, you were allowed more than 5% of the AGTI  as 80G deduction by the system (if your calculations and claims showed you were eligible), and raise a grievance, providing details of the previous AY deductions. Maybe if more tax payers raise the same grievance, the Department might recheck their software!

Sirs,

I also came across same issue of the system calculating or limiting the donation under 80G category to 5% of AGTI for the AY 2023-24 where as the rule position is clear that the donation amount under 80 G (with qualifying limit category) stating that  "50 of the donation amount"  or  " 10 of AGTI which ever is less" is eligible for deduction.  Even I checked up with some people who are familiar with Income Tax rules also.  When I raised a grievance for the above, the resolution given by them is "From the system we have noticed that you have already filed your return and the system will automatically process the return based on number of validations"

Even now in AY24- 25, this bug remains uncorrected !!!!!!. No way to edit in the online data