The flags mean that there is a room or yellow box that you haven't been to or opened in that level. If you find all the secrets in that level, the flag turns in a crown.
If you want 100% in the subspace emissary, you have to find all secrets.
A flag means that you have completed the level, but that there are still parts you have yet to explore, and likely orange box items you have yet to collect. The crowns indicate that the level has...
did not find and get all items in boxes that are in doors that may be hidden.
I remember a friend telling me it meant you did find everthing. Look for more hidden items in both stages with flags and...
I'm assuming you are stuck at a certain percent. The levels in the subspace emissary that have a flag (crown means complete) mean that you have missed something in that level, whether its a trophy or...