Was dkms working before you did the upgrade or was it already in a broken state?
wireguard-dkms-0.0.20190123-2.fc29.noarch won't fix an already broken install, so you
need to remove it and then install the new version. It should hopefully fix it moving
forward.
I started a thread on the WireGuard mailing list to track this issue
https://lists.zx2c4.com/pipermail/wireguard/2019-February/003851.html so please reply
there with any feedback once the next snapshot is released.
Thanks,
Joe