Well, one part of it is that Flatpak pulls data over the network, and sometimes data sent over a network doesn't arrive in the exact same shape as when it left the original system, which results in that same data being sent in multiple copies - until one manages to arrive correctly.
Hence why Fedora Linux actually recently removed delta updates for DNF. Turns out it used more data in retries than just downloading a whole package again.
Shoddy implementation they can't be arsed to fix. They do all kinds of shenanigans like show the size of all locales but only download one, or the other way around, it does not count dependencies and then realizes it has to download something extra etc. It's all over the place and I've given up on it making any sense. I've just made sure it's on a drive with plenty of space and hope for the best.