Radamel Falcao equalised for the visitors after former United trainee Ryan Shawcross had scored the first Premier League goal of 2015 in the second minute, but it was a third draw in four games for Louis van Gaal's side.
Palace's new signing Marouane Chamakh put the visitors ahead with a slickly taken goal in the first half, but Stoke scored twice in four second-half minutes to claim their first points of the season.
The home side were on the backfoot but managed to hold out for the draw against Roberto Martinez's men.
A statement from the FA also referred to two other clashes between Fellaini and Shawcross, but Halsey has confirmed he saw both and did not consider them violent conduct.
Rio Ferdinand was overlooked as John Terry's replacement in the England squad on Thursday, with uncapped center back Ryan Shawcross receiving his second international call-up.
Wales manager Chris Coleman will hold talks with captain Aaron Ramsey before deciding whether to call-up Stoke defender Ryan Shawcross, who was responsible for the tackle that left the Arsenal star with a badly broken leg.
