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Most of us use Calibre or transfer from a PC. Neither of which have any problems transferring epub or pdf files.You're apparently trying to transfer from your phone to Kindle using FTP. It's not entirely clear what you are doing since you are very reluctant to give much detail that would be needed to begin to troubleshoot anything.
You don't say what FTP program you were using, but FTP can transfer files in ASCII or binary mode. Some FTP programs default to ASCII, you need to ensure that you are using FTP binary mode.
Perhaps an easier way would be to use an OTG adapter/USB cable from your phone. An OTG adapter lets your phone act as a host (like a PC) and you should be able to simply transfer files with a file explorer like ES Explorer in the same way you would use windows file explorer.
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