interesting, i've never seen that.
on my system adb belongs to android-tools, and that packages does not come with a systemd service.
i only start it manually, and recently through a udev rule which doesn't work too well.

of course it could be the systemd service restarting itself for some weird reason...
you could show us the service file.

For me to adb comes in android-tools too.
And I set it to start at start-up with command 'systemctl enable adb'. (This means systemd starts it, right?)
What is service file?

Also for some reason I haven't had problems with other adb commands(shell, push, pull). I have pushed few ~2GB file without any problems.

EDIT:
I don't really know what I could try to do to find what causes the problem, so if there isn't some obvious files that I should check for info, I will just wait for Fedora 29 and do clean install.
I can just spam adb logcat untill it shows what I want.

ok, so you need an introduction into systemd basics.
but that's going a little off topic.

we haven't even begun to seriously troubleshoot this problem, as i believe i said earlier it isn't even sure if its source is on your phone or on the linux machine. could even be the cable for all i know.

sure, the next distro upgrade will fix everything. sweet dreams.

If you are willing and have time to provide some guidance, I sure would like to get it working, at least for learning purposes. I'll check about that systemd stuff tomorrow.
Same phone and same cable worked on virtual machine. I'm sharing net through usb at the same time, but I believe I did that with virtual machines too.

Is this the service file you meant, it was in 'usr/lib/systemd/system/adb.service'

yes.
now you need to compare this to other situations where it works, according to you.
you should also find out:

• what do the "PrivateTmp" and "Environment" options do
• what is the impact if you start this as root, but then continue to send commands as a normal user

i still maintain, don't use adb as root. there's just no need.
there's actually no need to autostart it at all.
the server will start automatically when the first adb command is executed.

PS:
a Quick Search (you should try it sometimes):
https://github.com/M0Rf30/android-udev-rules/issues/106
https://github.com/tweakdeveloper/adb-starter (that last one would disagree with me, but apparently there is an issue that needs to be addressed)

Upgrade to fedora 29 fixed the problem. Also now I would probably able to use adb normally without root access, if I set the plugdev group stuff.
In fedora 28 it didn't even show any errors(or anything else) if running without root and if android usb wasn't in "Transfer files" mode.

I always send commands as normal user after I start adb as root, and I used adb as a root because otherwise device won't be recognized at all.
With fedora 29 it gets recognized but has some permission errors. Which I don't know how to fix yet, but not a big problem because I can just keep running adb as root.
Doing quick search for a different problem is bit of a long shot.