Time to add some debugging statements to your code.
Serial.println(setCounter);
before you read incrementPin. This will show what it is and hence which setting the increment pin should affect. Expect it not to be what you think it should be due to key bounce as I mentioned before. Fix that in a crude way by reading the button twice with delay(50) between the reads to allow the bouncing to stop. There is a much better way to do it but that can wait.
Serial.println() some messages at various parts of your code so that you can keep track of where it is when it is running and what the values of variables are. Just before the 'if' tests is a good place.
One thing I did spot is that you have this
dayCounter++;
lcd.setCursor(15,0);
lcd.print(dayCounter);
if (dayCounter > 10)
{
freqCounter = 1;
}
2 things about that.
(1) deal with the rollover before outputting dayCounter (same problem with resetting setCounter after outputting it)
(2) you are resetting freqCounter to 1 when dayCounter goes over 10. I am sure that you can see why that is wrong
Fix those problems then if it still not working set setCounter to a fixed value as if the button had been read and see what happens