Hello! I have had this issue with a number of international files I have created for FM23 (as well as some made on FM21/22 that I converted).
@alian62's solution worked for my recreation of the Gulf Cup of Nations, but did not work for the other tournaments that had the issue. However, I did eventually get something that works so will share it here rather than open a new thread.
Building on @Shenmue-X's suggestion, I did the following:
Advanced Rules > Competition x > History > Team order for top 3 teams > Add
Select "Get Teams from Cup Round"
I then add competition name (might not be needed), maximum number of teams set to 2, and then relevant stage number and 'final' as round name
This has worked for international tournaments with a group stage then knockouts and also for tournaments with knockout rounds only. Might be worth a try for league/play-off systems with a similar issue. Note though that it only adds the two finalists. I haven't found a way to get third place play-off winners recognised yet.