Hmmm. Looks like your tournament was a site-wide one so my first reply was not of much use to you though it might apply to others who find this thread.
The system doesn’t take the decision(except in games vs bots). It offers a starting point to manually agree the score. The OGS documentation is currently being rewritten but I’ve taken the liberty of copying the relevant draft section:
Scoring (the stone removal phase)
When two consecutive passes occur, the game enters the stone removal phase. The OGS system automatically provides a preliminary scoring of the game. It does make mistakes, however. So the players then simultaneously make any needed corrections by clicking on stones or territory/area. This changes the status of the items. For example, stones and territory that you have captured will be marked as yours, or if the system has marked some of your stones as dead, when they are really in seki, you can reverse that marking. Clicking marks contiguous groups, while a shift-click will mark items one at a time.
Each time the game state is altered by either player, the internal clock for acceptance of the result is reset. When all stones are marked correctly click the “Accept removed stones” button. Once both players have accepted the result, the game concludes. If one of the players does not accept, nor offer differently marked position the current state is accepted after a period of time (depending on the time settings).
Game scores are final
Once both players have accepted the outcome of a game, there is no way to alter the game state (not even the administrators have this capability), so double check that everything looks right before you accept!
The Auto-score button will reset the state to the original preliminary scoring. It can be used in case a mistake is made during the process of correcting the score.
If you and your opponent cannot agree on the status of some stones, or if you missed something, you can click the Cancel and resume game button to pick up where you left off and continue playing the game. Two consecutive passes will again bring you back to the stone removal phase.
If the game cannot be resolved for whatever reason (e.g., if it is unclear whether a group is in seki), then pause the game by mutual consent and click the Call moderator button on the side panel.
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From your post my guess would be that this part in particular was unknown to you: