You can do as GoOnCal1 suggests and/or have a look at this for manually updating tournament information: https://www.pokertracker.com/guides/PT4/tutorials/tournament-auto-detection#updating-tournament-information-manually
For the issue of whether or not PokerTracker4 should be handling those differently it's best to open a support ticket here and send a couple original/unedited tournament hand histories and summaries if available (you don't need a pokertracker.com account for this, you can submit the ticket as a guest): https://www.pokertracker.com/contact/newticket.php?cat_id=2796
Make sure to send originals, not anything exported by PokerTracker4. Most likely the originals are somewhere in your PokerTracker4 processed folder here:
C:\Users\SOME_NAME\AppData\Local\PokerTracker 4\Processed
"SOME_NAME" will be your Windows username on that machine.
With the hand histories/summaries include a description of the trouble.