I’m not sure I understand what your issue is… The Skilled racial trait for humans has nothing to do with favored class. You gain a level, you get an extra skill point plane and simple… if you have been using your favored class bonus on HP, then so long as your level progression looks like the following for HP and Skills then you are fine…
HP per level = HD result + Con + 1 [FCB] + other (example: roughness)
Skills per level = 2/4/6/8 (dependent on class) + Int + 1
Allow me to rephrase the question…
What class are you playing and why is your intelligence modifier?
Allow me to rephrase the question…
What class are you playing and why is your intelligence modifier?
Currently Gunslinger 1/Trench Fighter 6.
Int is 14. No, I have not taken the extra skill point from skilled in my skills. I used it for the fighter's human favored class bonus.
I took the extra hp at each level as the character concept would go for toughness.
Then you should have 37 total skill points right now… 6 from gunslinger, 24 from fighter, and 7 from skilled… if you don’t then you should talk to your DM about correcting it… by the sounds of it you are probably just 1 short… how you were tracking it is irrelevant so long as the total is correct.
Int is 14. No, I have not taken the extra skill point from skilled in my skills. I used it for the fighter's human favored class bonus.
The Human's Racial Trait 'Skilled' is a completely different ability than the Favored Class Bonus. They do not interact in any shape or form.
You can not spend the bonus skill ranks from Skilled to instead select a Favored Class Bonus.
As a human you get 1 extra skill point per level no matter what class you take. The class does not need to be your favored class you get it for any class including prestige classes. This has nothing to do with the favored class bonus.
If you take a level in your favored class you get to choose between +1 HP, +1 skill point or the alternative favored class bonus of your race. You can choose any of the bonuses and can even change them from level to level.
There is nothing wrong with choosing the HP as a human. A human gunslinger should be getting 5 skill points just for being a human. Your INT boost that number to 7 per level. This is how many skill points per level you should have if you used the favored class bonus for HP.