The 33-year-old forward reacted angrily to a challenge from Arteta and appeared to strike the Spaniard in the back.
Referee Chris Foy failed to book Owen over the incident and Pulis thinks that it is something that the governing body might look at after the weekend.
"If Michael has done what he has done and they look at it, then they will deal with it," Pulis told the BBC.
"We'll see what they say. Obviously I am going to be biased as it is my football team. Arteta's challenge was poor, but Michael should not do that."
The defeat leaves Stoke in 10th position in the Premier League after picking up 30 points from 25 games.