Discussed with second bank, they are aware of the issue and they are claiming, - "3D-Secure authentication, or three-step verification, works if the merchant has also joined this system. Merchants who have joined the 3DS security system will display a logo on their website with the words "Mastercard SecureCode" and / or "Verified by Visa". If you see the corresponding logos, it means that the merchant has taken more responsibility for his customers and is likely to be required to identify the card.
And according to the - https://support.apple.com/en-us/HT202527 Apple uses it.
So now Apple is requiring from the banks 3D-Secure authentication, but Apple is unable to understand or display to the customers three-step verification request. And as request won't pass the first step (Mastercard verify user screen?), the final request wont reach the bank at all, so that's why bank can't see any requests and that's why local banks don't have any logs.
So this is clearly Apple -s fault and all banks clients are suffering and even more, Apple looses money.