Several packages of Fedora 41 remained after system upgrade to 42

$ dnf list --installed | grep fc41
bison.x86_64                                         3.8.2-9.fc41                        fedora
cogl.x86_64                                          1.22.8-11.fc41                      anaconda
dbus-glib.x86_64                                     0.112-9.fc41                        anaconda
gtk2.x86_64                                          2.24.33-19.fc41                     anaconda
gtk2-immodule-xim.x86_64                             2.24.33-19.fc41                     anaconda
ipxe-roms-qemu.noarch                                20240119-2.gitde8a0821.fc41         fedora
iscsi-initiator-utils.x86_64                         6.2.1.10-0.gitd0f04ae.fc41.1        anaconda
iscsi-initiator-utils-iscsiuio.x86_64                6.2.1.10-0.gitd0f04ae.fc41.1        anaconda
libblkio.x86_64                                      1.5.0-2.fc41                        fedora
libldm.x86_64                                        0.2.4-16.fc41                       fedora
liblouisutdml.x86_64                                 2.12.0-3.fc41                       anaconda
liblouisutdml-utils.x86_64                           2.12.0-3.fc41                       anaconda
liblqr-1.x86_64                                      0.4.2-25.fc41                       anaconda
libseccomp.x86_64                                    2.5.5-2.fc41                        anaconda
libvisual.x86_64                                     1:0.4.1-5.fc41                      anaconda
openexr-libs.x86_64                                  3.2.4-3.fc41                        anaconda
thrift.x86_64                                        0.20.0-3.fc41                       fedora
vpnc.x86_64                                          0.5.3-48.svn550.fc41                anaconda
xl2tpd.x86_64                                        1.3.17-6.fc41                       anaconda
zimg.x86_64                                          3.0.5-3.fc41                        anaconda

$ dnf repolist
repo id                                                    repo name                                                                
code                                                       Visual Studio Code                                                       
copr:copr.fedorainfracloud.org:dsommers:openvpn3           Copr repo for openvpn3 owned by dsommers                                 
fedora                                                     Fedora 42 - x86_64                                                       
fedora-cisco-openh264                                      Fedora 42 openh264 (From Cisco) - x86_64                                 
rpmfusion-free                                             RPM Fusion for Fedora 42 - Free                                          
rpmfusion-free-updates                                     RPM Fusion for Fedora 42 - Free - Updates                                
rpmfusion-nonfree                                          RPM Fusion for Fedora 42 - Nonfree                                       
rpmfusion-nonfree-updates                                  RPM Fusion for Fedora 42 - Nonfree - Updates                             
terra                                                      Terra 42                                                                 
updates                                                    Fedora 42 - x86_64 - Updates      

If I remove, for instanse the bison package and then install it again by a command like sudo dnf install bison it brings me exactly the same version. Could someone explain why or is it ok?

The Fedora upgrade procedure was done according to Upgrading Fedora Linux Using DNF System Plugin :: Fedora Docs

It is OK. The Fedora 42 repository contains quite a few packages with the .41 suffix and even some with a .40 suffix. Someone needs to change a specification file to change the suffix to .42 and for some packages that has not happened.