That is a limitation of the anonymous names system which allows the Hud to reset stats when players change at the table.
The hole card information from downloaded hands will be updated over generated hands when possible, but this requires being able to match up the player names.
We give the anonymous players "random" names based on when they are first seen in a hand. These names are not actually random but are generated consistently based on the time of the first hand in which a player is seen (so that re-importing the same file gives the same names every time).
Generated hand histories often include some observed hands at the start of a session while you're waiting to post the blinds, and these hands are not included in the downloaded histories.
In the generated hands you first encountered these opponents at a different time to the time of the first played hand in the downloaded history, so when importing the downloaded history afterwards this generates a different "random" name for those opponents, meaning that when we try to update the hole card information in the database we can't match the player name to the one already in the database.
Furthermore, if a player sits out but does not leave the table until a later hand the downloaded history does not tell us which player left so the names cannot be reset in that case. The grabbed hands include this information to generate more accurate player stats. This causes another discrepency in the generated names.
The development team debated ignoring observed hands to avoid this problem, but decided that it would be more beneficial to have stats from those few hands available in the Hud when first being dealt in, especially since you don't have any stats from previous sessions for anonymous players.
When names are anonymous knowing the hole cards your opponents had doesn't really tell you anything since you can't learn anything about a player to use in the future (because you don't know who it is), and you can't judge how you played the hand (or could have played the hand better) based on information that you didn't have at the time.
That said, if the development team are able to find a way to match up the hole card info to the correct player in the future I'm sure they'll do that.
If you want to analyze the full hole card data we recommend creating a separate database to import the downloaded hands.