There are various different uses of the number 12 across the Marvel Cinematic Universe:
Does it have any significance at all or is it a running gag?
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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.
It was something they started in Avengers, but James Gunn kept in Guardians because he thought it was funny.
James Gunn keeps Joss Whedon’s joke going, with Star-Lord informing the rest of his team that he has a plan for the film’s third act. Well, 12% of a plan. The idea is once again ridiculous to Rocket Raccon (Bradley Cooper), with Gamora (Zoe Saldana) explaining that 12% isn’t a plan – it’s “barely a concept.”