Linux – Size difference between an iso file burnt to a cd and the file retrieved with dd

It will not be possible without repacking the ISO into two separate ones.

There is only one Primary Volume Descriptor in the ISO image by which the readers can find the tree of directories and files.

You would have at least to create a second such PVD and a second directory tree, which allow access to the files on the second DVD. Further you would have to remove those files from the first directory tree which get stored on the second DVD. Else you get i/o errors when trying to read those files.

Your usb stick has failed.

Some drives return different sizes when they fail, although I've only read about this with regard to "SSDs", which have more complex controllers.

To double-check the size of the drive as a whole, I would use lsblk or look in the kernel log dmesg. (The size of partitions within the device could be completely bogus depending on the partition table; you could contrive this without having a hardware failure).

If the size was OK, there are ways you could try to recover important data. But it doesn't sound like you need to - you still have access to the Kali ISO file.

Simple usb sticks aren't designed with any extra hardware diagnostics[*]. Once you know the hardware has failed, that's it. Either of the size of the drive as a whole going wrong, or the drive not returning the data you wrote to them (suggested by failure of fdisk), would be enough to indicate such failure.

[*] I think they're not even designed for uses where the maximum expected re-write cycles of flash storage becomes an issue. They're much more likely to just break, or be lost.