The 22-year-old thought he heard referee Andy Davies blow for a foul by team-mate Steven Cook on the edge of the penalty area and picked the ball up inside the box.
Davies pointed to the spot and Will Gregg wrapped up the three points but Howe was adamant the former Torquay midfielder was not to blame.
"It was a free-kick, it should never have been a penalty," Howe told BBC Radio Solent.
"You can't attach any blame to Eunan, he's picked the ball up almost in good faith really. It was a bizarre incident really. I mean it was clearest free-kick you'll ever see.
"Steven Cook's almost in desperation because he's been done by the centre forward, who's hacked him down to almost stop him coming into the box, rightly or wrongly.
"Everyone in the ground expected a free-kick, Eunan's heard a phantom whistle and he's picked the ball up. It's something he'll learn from. I don't think he'll ever do it again."