There is no significance, and it doesn't seem to be a running gag either.

As per this twitter conversation between a fan and Guardians of the Galaxy director James Gunn;

"Hey @JamesGunn was Star Lord's 12% plan from GoTG a deliberate reference to Stark's 12% credit from Avengers or was it a happy coincidence?" "No. The number 12 is often used in writing/comedy because it's the highest one syllable number."

So there is no significance to the number 12 in these films. It just so happens that the way it sounds makes it convenient to use in a joke, and both directors have.