Rotherham assistant manager Paul Raynor believed his side were denied a certain penalty.
A last-minute equaliser by Danny Ward dampened the first game in charge for new Charlton manager Guy Luzon, leaving them still waiting for their first win at home since October.
With manager Steve Evans locked in discussions with referee Scott Duncan, Raynor was angry with a handball decision not given against Andre Bikey.
“They say things even themselves out over the season, and we are going to get some penalties if that is the case,” he said. “The handball is absolutely blatant, sometimes it is difficult to see from the dugout but there was no guesswork today.”
The game was settled with two goals in the last 10 minutes.
However, both sides hit the woodwork in an otherwise disappointing first half. Ben Pringle was picked out at the back post after seven minutes, but saw his shot bounce off the post.
Johann Gudmundsson lobbed over Adam Collin on 18 minutes but the ball ricocheted off the upright and into the arms of the goalkeeper.
The handball decision on 68 minutes not given by referee Duncan clearly incensed Rotherham and the mood of the visitors was blackened even further with seven minutes remaining, when Jordan Cousins struck the ball home from six yards out.
However, Rotherham were rewarded for their effort when Ward equalised in stoppage time after the home side failed to deal with a high ball into the box.
Charlton Athletic: Dmitrovic, Solly, Ben Haim, Bikey, Wiggins, Gudmundsson; Buyens, Veljkovic (Lepoint 80), Cousins, Vetokele (Watt 63); Harriott (Gomez 89). Unused substitutes: Wilson, Onyewu, Fox, Etheridge.
Rotherham United: Collin, Richardson, Morgan, Arnason, Fryers; Newton (Hunt 60), Green, Smallwood, Pringle (Hammill 80); Sammon (Ward 76), Derbyshire. Unused substitutes: Wood, Bowery, Barmby, Thompson.
Referee: S Duncan (Tyne & Wear).
Man of the match: Danny Ward.