The 1-1 Sky Bet Championship draw at the Cardiff City Stadium saw a Reading fan ejected in the first half by stewards for making an offensive gesture, while a supporter raced onto the pitch from a home section after the Bluebirds equalised 20 minutes from time.
Last weekend, the FA Cup fourth-round tie between the two clubs at Reading saw four Cardiff supporters arrested by Thames Valley Police on suspicion of racist chanting under the Football Spectators Act.
"Unfortunately, you are never going to stop single individuals, maybe if they have had a drink too many, coming out with ridiculous things," Neath-born Bowen said.
"It never stops. We all pray it will, but it never does.
"Thankfully, they are isolated incidents. I grew up with Cardiff fans, living just down the road from them, they are a vociferous lot and they really get behind their team.
"We have away fans who try and do the same things as well."
Cardiff and Reading will meet for the third time in 10 days on Tuesday in their FA Cup replay.
There certainly appeared to be some settling of scores in a committed contest that threatened to boil over at times.
"It was a feisty affair, but the referee handled it well in my opinion," Bowen said.
"There were one or two running battles on the pitch, familiarity breeds contempt.
"But like good professionals they came off the pitch and shook hands and said 'see you on Tuesday'."
Yakou Meite headed Reading into an eighth-minute lead before Callum Paterson levelled with his third goal in as many games.
On the first-half crowd incident with the Reading fan, Cardiff manager Neil Harris said: "I heard a raised level of noise, I didn't see what went on with the stewards.
"I can't comment because I'm not aware of what went on.
"At the time I was thinking about getting my team back into the game, I'm not sitting on the fence."
Cardiff completed the signings of Nottingham Forest winger Albert Adomah and Wolves defender Dion Sanderson after the game and just before the 11pm transfer deadline.
Lee Peltier's five-season stay at the club came to an end as the full-back joined West Brom.
"Sometimes you have to say thank you and well done for what you've done here and good luck to new challenges."