I am trying to upgrade my mikrotik router and after successfully rebooting, I am still in the old version. Is there any way I can troubleshoot this?

Is there anything in the logs ?

Nope. The logs are clear of any failure message.

I have downloaded a new firmware and manually installed it, tried to install a beta or a stable version etc.

I've even tried the disk space patch by Mikrotik. It still reboots and I am in the same version.

The only suspicious thing is that I have two "security" packages in the Packages section, both disabled. I am trying to enable the first and uninstall the second but it doesn't work.
There are still there, no matter what I am choosing.

Make sure you have set the logging to disk and try again

I see things in logs but only related to connections and networking. What am I expecting to see?

The only suspicious thing is that I have two "security" packages in the Packages section, both disabled. I am trying to enable the first and uninstall the second but it doesn't work.
There are still there, no matter what I am choosing.

There have been numerous reports about duplicate packages installed (one from bundle and one from separate package) and such state doesn't allow administrator to do anything related to packages (including up&down grade). The only solution out of such mess seems to be netinstall. You can save a fresh backup before start, then netinstall device with the same version of ROS (this should fix duplicate packages), restore config and then proceed with ROS upgrade.

That was really good. I guess that it seems hard from the outside but If you go through the process once, it's just easy as a game.

Backed up, netinstalled, Restore - All systems running and updated. The more I get used to it and fix problems, the more I love it.

Thank you.

I can confirm that.
I have 2 devices who are not possibility to update/downgrade at all. They are works properly.
Logs give me only info about "system,error,critical router was rebooted without proper shutdown" - I reboot it from WinBox&CLI etc. and no any effect.

NETINSTALL fix all.