The 30-year-old club captain was making a return from a hamstring injury which has kept him out of the Millers picture since the 2-1 defeat at Preston on January 2 - a run of four games.
He was named in the starting XI for the second-string outing at Glanford Park on Tuesday night in an attempt to build his fitness ahead of Saturday's vital clash with Charlton but he only lasted 43 minutes before replaced.
However, the problem did not appear to be too serious, though he was tended to by Denis Circuit after going off, and his removal is thought to be a precaution.
A recurrence would be the latest in a long line of injury problems for Frecklington, who has been restricted to just 16 appearances this season.
The midfielder spent two months out with a troublesome calf problem and also spent long periods in the treatment last campaign.
The Millers did receive some positive news from their 3-1 victory against the Iron as Luciano Becchio continued to build his match fitness.
The Argentinian played 90 minutes and got on the scoresheet, as did fellow striker Jonson Clarke-Harris, who staked his claim for a starting berth against the Addicks on Saturday.
Meanwhile, defender Aimen Belaid is expected to be fit for that clash after he limped out of the 2-2 draw with Cardiff on Saturday.
The Tunisia international hobbled off in the final 10 minutes in south Wales but boss Neil Redfearn is not concerned.
"He just had a bit of tightness in his groin so hopefully
we've got him off in time, before it did any real damage."
