Madrid were made to work hard for a 1-0 victory on Sunday - their seventh win in a row - as Zinedine Zidane's men moved seven points clear at the top of the LaLiga table.
But Athletic were unhappy with the award of the spot-kick from which Ramos clinched the points, with Dani Garcia's trip on Marcelo spotted only after a VAR review.
Muniain was particularly frustrated as there was then no similar call made at the other end of the pitch when Ramos appeared to step on Raul Garcia's foot off the ball.
He said: "Raul Garcia has been stamped on and they haven't even reviewed it. That's the difference.
"We've seen the theme in these weeks since the restart - depending on which teams it is, some decisions are given.
"Everyone can draw their own conclusions."
Those claims prompted Ramos to respond: "People shouldn't be imagining things!"