When downloading large files like a Linux distribution things can go wrong, one little error can produce steam out of your ears. That's why Linux distributions compare the md5 or sha1 sums or both of every file sitting on the server for that ISO to the files in the ISO on your drive. One of those files is an MD5 or SHA1 text file containing the sum for every file in the ISO, if you remove files, you'll need to edit that file to reflect the changes.
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For Windows OS making bootable disks is not a problem since there is no checksum verification
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Probably because Windows is normally distributed on disks and not the internet, the sums have been verified prior to including them on the disk.
There is usually a sort of "autorun" application that loads when inserting an OS installation disk, in Linux it's commonly called "the installer". If you remove some of the features the installer is programmed to include in some way, you might have issues in that arena also.