I got the latest stable kernel update on my machine and updated. I got the same issue but when I tried to update my VM I couldn't reproduce it so I changed the "Reproducible" status to "Happens sometimes, but not always.". 

At this point I am afraid I don't know the root cause of this so I am going to explain in what state my system is, so it may help. Since I figured out I have a kernel issue on the latest versions I decided to use an older kernel and try to use a RC kernel, so that's where it all started. I started to play with kernels update/remove etc. and I noticed this issue. When I got the latest stable kernel update today running "sudo dnf autoremove" wanted to remove "kernel-modules-extra" again. I installed the rawhide kernel again and now dnf autoremove doesn't want to remove "kernel-modules-extra" anymore. I am not sure if I will see this issue again in the next kernel update. 

One more thing I want to add here is I did run "sudo rpm --rebuilddb" on the VM before today's latest stable kernel update could that explain why I couldn't reproduce this on the VM meanwhile I could on my main system?

Please could you provide an output from:
dnf repoquery 'kernel*'  --qf '%{name}-%{epoch}:%{version}-%{release}.%{arch} %{reason}' --installed

dnf repoquery --whatrequires 'kernel-modules-extra' --installed

Output from "dnf repoquery 'kernel*'  --qf '%{name}-%{epoch}:%{version}-%{release}.%{arch} %{reason}' --installed":

kernel-0:5.10.12-200.fc33.x86_64 user
kernel-0:5.10.8-200.fc33.x86_64 user
kernel-0:5.11.0-0.rc6.141.fc34.x86_64 user
kernel-core-0:5.10.12-200.fc33.x86_64 user
kernel-core-0:5.10.8-200.fc33.x86_64 user
kernel-core-0:5.11.0-0.rc6.141.fc34.x86_64 user
kernel-headers-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.12-200.fc33.x86_64 user
kernel-modules-0:5.10.8-200.fc33.x86_64 user
kernel-modules-0:5.11.0-0.rc6.141.fc34.x86_64 user
kernel-modules-extra-0:5.10.12-200.fc33.x86_64 user
kernel-modules-extra-0:5.10.8-200.fc33.x86_64 user
kernel-modules-extra-0:5.11.0-0.rc6.141.fc34.x86_64 user

Output from "dnf repoquery --whatrequires 'kernel-modules-extra' --installed":

(There is no output)

One thing I want to add is when I was running these commands "sudo dnf autoremove" don't wanted to uninstall "kernel-modules-extra" I saved those commands and next time when I can reproduce that "sudo dnf autoremove" wants to remove "kernel-modules-extra" I will share output from that scenario too.

I removed some of my kernels and downgraded to latest stable and could reproduce it. 

Output from "dnf repoquery 'kernel*'  --qf '%{name}-%{epoch}:%{version}-%{release}.%{arch} %{reason}' --installed":

kernel-0:5.10.11-200.fc33.x86_64 dependency
kernel-0:5.10.8-200.fc33.x86_64 dependency
kernel-core-0:5.10.11-200.fc33.x86_64 dependency
kernel-core-0:5.10.8-200.fc33.x86_64 dependency
kernel-headers-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.8-200.fc33.x86_64 dependency
kernel-modules-extra-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-extra-0:5.10.8-200.fc33.x86_64 dependency

Output from "dnf repoquery --whatrequires 'kernel-modules-extra' --installed":

(Still here is no output)

Here is an image: https://i.imgur.com/VrLLaPp.png (can see all the commands + sudo dnf autoremove)
https://i.vgy.me/qJllNS.png (alternative image link in case one hoster as an issue)

Please could you provide all steps that you performed to get from state from commend 3 to state in comment 4? Minimal reproducer will be very helpful.

To get to state in comment 3 you can run `dnf mark install kernel kernel-core kernel-modules-extra kernel-modules`

I can confirm that there is an issue in dnf, but a different one that was reported.
When kernels are user installed and I remove one of kernels, the all remaining have reason unknown. But I am unable to reproduce switch from user to dependency reason.

I could finally reproduce! So the issue is that when you are in unknown state and then install "sudo dnf config-manager --add-repo=http://dl.fedoraproject.org/pub/alt/rawhide-kernel-nodebug/fedora-rawhide-kernel-nodebug.repo" nodebug repository and run "sudo dnf upgrade" it will install the kernel and when you run "dnf repoquery 'kernel*'  --qf '%{name}-%{epoch}:%{version}-%{release}.%{arch} %{reason}' --installed" you then should be in the dependency state. At that point running "sudo dnf autoremove" will try to uninstall "kernel-modules-extra" packages. 

A more step by step:

1) My current state:
kernel-0:5.10.11-200.fc33.x86_64 user
kernel-0:5.10.8-200.fc33.x86_64 user
kernel-0:5.11.0-0.rc6.141.fc34.x86_64 user
kernel-core-0:5.10.11-200.fc33.x86_64 user
kernel-core-0:5.10.8-200.fc33.x86_64 user
kernel-core-0:5.11.0-0.rc6.141.fc34.x86_64 user
kernel-headers-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.11-200.fc33.x86_64 user
kernel-modules-0:5.10.8-200.fc33.x86_64 user
kernel-modules-0:5.11.0-0.rc6.141.fc34.x86_64 user
kernel-modules-extra-0:5.10.11-200.fc33.x86_64 user
kernel-modules-extra-0:5.10.8-200.fc33.x86_64 user
kernel-modules-extra-0:5.11.0-0.rc6.141.fc34.x86_64 user

2) "sudo dnf remove kernel-core-5.11.0-0.rc6.141.fc34.x86_64" (this was a locally installed one)

3) Removing that locally installed kernel will make you fall into unknown state. 
kernel-0:5.10.11-200.fc33.x86_64 unknown
kernel-0:5.10.8-200.fc33.x86_64 unknown
kernel-core-0:5.10.11-200.fc33.x86_64 unknown
kernel-core-0:5.10.8-200.fc33.x86_64 unknown
kernel-headers-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.11-200.fc33.x86_64 unknown
kernel-modules-0:5.10.8-200.fc33.x86_64 unknown
kernel-modules-extra-0:5.10.11-200.fc33.x86_64 unknown
kernel-modules-extra-0:5.10.8-200.fc33.x86_64 unknown

4) "sudo dnf config-manager --add-repo=http://dl.fedoraproject.org/pub/alt/rawhide-kernel-nodebug/fedora-rawhide-kernel-nodebug.repo" and "sudo dnf upgrade" (install the kernel)

5) After installation of the nodebug kernel from the repository you should be in the dependency state.
kernel-0:5.10.11-200.fc33.x86_64 dependency
kernel-0:5.10.8-200.fc33.x86_64 dependency
kernel-0:5.11.0-0.rc6.141.fc34.x86_64 dependency
kernel-core-0:5.10.11-200.fc33.x86_64 dependency
kernel-core-0:5.10.8-200.fc33.x86_64 dependency
kernel-core-0:5.11.0-0.rc6.141.fc34.x86_64 dependency
kernel-headers-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-0:5.10.8-200.fc33.x86_64 dependency
kernel-modules-0:5.11.0-0.rc6.141.fc34.x86_64 dependency
kernel-modules-extra-0:5.10.11-200.fc33.x86_64 dependency
kernel-modules-extra-0:5.10.8-200.fc33.x86_64 dependency
kernel-modules-extra-0:5.11.0-0.rc6.141.fc34.x86_64 dependency

6) Try to run "sudo dnf autoremove" and see that it will try to remove "kernel-modules-extra"

Hope this one helps. Thanks.

Thanks a lot for detail information. I can reproduce it and we are looking for a solution.

I create a patch that helps with the problem (https://github.com/rpm-software-management/ci-dnf-stack/pull/958). It prevents reason change from unknown to dependency, therefore the issue with autoremove will disappear. But there is still a problem with change from user to unknown.

Tests:  rpm-software-management/ci-dnf-stack#958

Also requires: Requires: https://github.com/rpm-software-management/dnf#1728

I forget to add a reference for main part of the patch - https://github.com/rpm-software-management/libdnf/pull/1141

FEDORA-2021-447fb19490 has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2021-447fb19490

FEDORA-2021-447fb19490 has been pushed to the Fedora 33 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --advisory=FEDORA-2021-447fb19490`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2021-447fb19490

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

FEDORA-2021-447fb19490 has been pushed to the Fedora 33 stable repository.
If problem still persists, please make note of it in this bug report.