The Missions page tells you that the gray loop bonus is independent from the red loop bonus. This means they have nothing to do with each other. This does not mean you can only earn one. You can earn both.
Here is the mission #23 refers to:
LOOPS - Required Condition: Loops need to be in Base.
BONUS: New technologies can sometimes eliminate your need to travel. They are hard to develop, but each new one makes the next come easier... If all three gray loops have reached Base, you may take one red loop into Base by hand. Independent from that, if all three red loops have reached Base, you may take one loop of any color into Base by hand. Once earned, these hand freedoms (which are a special exception to the rules) may be used any time before the match ends.
The Inventioneers: Remember - if your robot gets all three gray loops back to base, you get one red by hand. If you get all three red (which you can do if your robot brings all three gray loops and two red loops back to base then the third red by hand), you can pick any remaining loop on the table to bring to base by hand. Or you can just retrieve all the reds with your robot and pick up one loop of any color by hand.
24 - BROKEN LOOPS
Regarding benefit-of-the-doubt calls for broken loops (as provided in QA22) - At the south wall, the referee needs to see a LIFTING attempt in order to doubt the loop or its setup. When a loop breaks after a tried/failed lift attempt, if the robot can get part of it to Base, it will score. Pulling on it sideways, back & forth, etc., until it snaps will be seen as intentional field damage, and any portion that reaches Base will be taken off the field (no score).
The Inventioneers: Again, the referees will be looking to see that your robot is following the spirit of the game - honest attempts to complete the missions using hardware and software strategies to accomplish the tasks. Just bulldozing your way through is not in the spirit of the game. Mission models can and do break during the game but don't count on it as a strategy. Not only has Scott Evans made deliberate field damage clearly prohibited, you shouldn't count on every mission model on every table to behave the same way. Remember at tournaments, the models may even be glued!