This image needs to be posted more recklessly
Note that the color does not represent the ones in the field.
I jumped into the game and took some shots to explain what's going on in the HUD:
This is your safe zone around the onion. All Pikmin in this circle are SAFE. Even if you haven't plucked them (or especially if you haven't plucked them as buried Pikmin are safe ANYWHERE as they cannot be eaten when buried).
This is your End-of-Day-HUD. As Zeer0id mentioned, the indicator in the top right appears during the "Hurry Up!"-part of the day to show you how many Pikmin you will lose if you don't find them. The indicator is always a Red Pikmin, no matter which type is left out in the field. As you can see, there are currently 11 Pikmin Nintendoomed to die.
Now this is your map screen during the End-of-Day phase and it has been updated with an additional HUD-element: the very important "alright WHO is missing?" indicator, telling you exactly how many Pikmin of each type are out in the field unattended.
If you compare the last two shots, you can see that there are currently zero Yellow Pikmin unaccounted for even though Alph is player controlled right now, Brittany is in the safe zone and Charlie is just standing there. But Charlie does have the Yellow Pikmin behind him dancing to his whistle. Thus, they are counted as SAFE, no matter where Charlie is.
Only the singular Rock Pikmin, the three Blue Pikmin, four Winged Pikmin and three Red Pikmin will find themselves in a big ol' Bulborb sandwich bar as "special" dinner guests.