Each character can only have ONE favored class. Even races that have 2 favored classes state the choice between the two classes "must be made at 1st level and cannot be changed".
Note that there is no mention that whatever class You choose at 1st level is automatically Your favored class. Therefore, a 1st-level Human could select Fighter as their favored class yet take Rogue at 1st level. (Being a fighter is the character's true-calling, but they grew up on the streets as a pickpocket and didn't find that calling until later in life.)
Where a Gestalt is concerned, remember that if both classes offer the same feature, You take only the better one. i.e. Hit Dice, BAB, etc.
If one of the two classes taken at a given level is the character's favored class, that means that class is granting them a favored bonus — something the other class isn't. Therefore, at any such character level where one of the two classes taken is the favored one, the character gets that benefit.
If for some reason You allowed for a single character to have multiple favored classes, (i.e. an elven ranger/wizard) then each class has a favored class bonus it is trying to grant. Since this is a case where both classes are granting the same ability, You only get it once.
Why?
The Favored Class is a racial ability that [essentially] grants a class ability. Gestalts get multiple class ablities at each level, not extra racial abilities.
In summary, even a Gestalt would have only one favored class and they'd gain +1HP or +1SP at any character level at which they take a level in that favored class. At no level could a Gestalt gain +2 HP/SP or +1HP & +1SP due to the favored class mechanic. Nor would being a Gestalt prevent such a character from gaining their favored class bonus if applicable.
