Both sides ended with 10 men, with Colchester midfielder David Perkins first to go after he handled on the goalline and Charlton striker Benson seeing red for his 88th-minute challenge on home defender John White.
Goals from Matt Heath and Andy Bond were cancelled out by two Johnnie Jackson penalties for Charlton against his former club, and after Anthony Wordsworth had given Colchester the lead for a third time, Benson drilled home another equaliser in the 76th minute.
Parkinson said: "I've had some eventful games when I've come back to Colchester. We got a point, which is ok, but it should have been three.
"It's so frustrating because I thought the lads did well and it was difficult to come here, especially after Wednesday's game (against Brighton).
"We will definitely appeal the red card. I'd be very surprised if it doesn't get overturned because there was minimal contact there. If it stands I think we've all got problems because there would only be about seven players left on the pitch if you get sent off."