Hello bisenberger,
Green flag is used for pinned marker position, it indicated that markers projection was manually specified or refined by user.
Blue flag is used for projections estimated by PhotoScan automatically - in case of Guided marker approach placement, for example, or Track markers procedure for multi-frame chunks.
And grey flags indicates estimated position for marker based on it's projections on photos that were already aligned.
Blue and green flags are used for referencing and/or optimization, whereas grey flags are not. Grey flags have only visualization purpose to help user to find estimated marker projection.