There's nothing in your code that immediately leaps out at me as being the cause. Had you shown your messages, that may have helped. Also, "it add some extra space" isn't all that useful: disk space? whitespace? how much extra? Furthermore, you included a lot of additional code (database, digest, options) that's irrelevant to the problem: this neither helps nor provides a script we can run to attempt to reproduce your problem.

Here's some things you can try:

• See how the data being added relates to the actual file: 1 byte might suggest an end-of-file issue; bytes == lines might suggest an end-of-line issue; some other relationship might suggest something else.
• If you have access to both servers, login and check (e.g. with ls) whether the sizes reported by your program match the sizes reported by the OS.
• Look at the files (e.g. with cat -vet, hexdump, or similar tools) and see how they differ.
• Check whether your source data contains Unicode. If so, look for encoding issues: remembering that ASCII characters are one byte, while Unicode characters are one or more bytes.
• Write a test script, which is a stripped down version of what you posted, such that it just contains barebones FTP transfer code. Then, using a small, but representative, example of your real data, attempt to reproduce your problem. Doing this may highlight the problem for you; if not, post that minimal script and we can look at it further.

Finally, and unrelated to your posted issue, instead of "loop: { ... goto loop }", consider:

while (1) {
    ...
    last unless @tree;
}
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