A third straight defeat for the Hammers saw them bundled out of the League Cup 3-2 at Molineux.
Afterwards, Bowen had to be held back by teammates after becoming incensed by comments from away supporters when going across to applaud them after the final whistle.
Following the incident and defeat, Potter said: "We're all in pain so we need everybody to help, we need everybody's support, we need to push forward and on to the next match.
"The team's suffering at the moment, we all are, we're all hurting. I can assure you no-one's happy.
"I have no idea what was said or anything. Our supporters have been fantastic, they are hurting because of the results we've had and Jarrod obviously cares about the club and the team. It's just an exchange of views by people who care.
"Everyone is hurting, rightly so because we haven't had the results we'd like. Jarrod has been a fantastic captain and servant for the club."
Apologies
Meanwhile, later in the evening, Bowen took to social media to apologise for his actions.
"Apologies to the fans for tonight's reaction," the England forward wrote.
"I'm someone who is passionate and will fight every time I step on the pitch. But I need to set a better example and you fans know how much I love you and this club.
"We ride through the bad times together and I'll see you all Sunday."