In September he got a two-game ban for allegedly swearing at Pakistan-born Sussex batsman Ashar Zaidi and telling him to "get back to your own country".
However, Yorkshire's Andrew Gale missed four games after a similar exchange with South African Ashwell Prince.
Coach Jason Gillespie says Yorkshire will probably "seek clarification".
New details of the Overton case emerged in a report in the Guardian.
All ECB cases are handled by an independent body, the Cricket Discipline Commission.
Yorkshire captain Gale was initially banned for two matches for the incident involving Prince in 2014, but the CDC decided to extend the suspension by two further games.
Overton, 21, who has been part of England's one-day squad and came close to selection for the winter Test tour to South Africa, was found guilty of a level one offence for abusive language.
He reportedly denied the claims concerning the incident, which occurred during Somerset's Championship game with Sussex in September.
The ECB also denied Overton received favourable treatment, after he was picked for the England Performance Programme (EPP), which will travel overseas this winter.
"After reviewing the umpires' report, the chairman of the CDC gave clear guidance that this should be reported as a level one offence and that no further action would be taken by the CDC," the ECB said in a statement.
"The automatic penalty for a level one offence was subsequently applied and this took Craig Overton to nine points, the threshold for an automatic suspension.
"Craig Overton's selection for the EPP squad would have played no part whatsoever in the CDC's ruling in this matter. The ECB refutes any suggestion of interference or bias in the proper disciplinary process."
Before the England team left for their winter tour of South Africa, Test captain Alastair Cook said he did not know about the case but added: "Everyone knows the responsibility we have when you pull on that England shirt.
"Of course you want everyone to be committed and give everything for the cause but there is always a line you should not go past."
Somerset chairman Andy Nash added: "The matter is closed as far as we're concerned. I think the ECB dealt with it entirely satisfactorily, and we will always abide by and respect the ECB disciplinary committee".

The special, called The Return of Doctor Mysterio, will be shown on BBC One on Christmas Day.
It sees The Doctor working together with a superhero called Doctor Mysterio to save New York from a deadly alien threat.
The dynamic duo will be joined on their quest by an investigative journalist, played by actress Charity Wakefield.
The mysterious Doctor Mysterio will be played by actor Justin Chatwin, and the episode will be written by Steven Moffat.
Writer Steven Moffat said: "I've always loved superheroes and this Christmas Doctor Who dives into that world. My favourite superhero is Clark Kent. Not Superman, Clark Kent."
Matt Lucas, who said he would return to Doctor Who earlier this year, will also appear in this episode.

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11 October 2014 Last updated at 16:05 BST
Duncan Wilson, chief executive of Alexandra Palace and Park says at the moment it is one of London's "least well known architectural treasures".
The world's first television station could be renovated too under the plans, as John Thompson of Alexandra Palace Television Group explains.
Jim Wheble reports.

The 27-year old made the podium at Rio 2016 in the men's 85kg category with a lift of 390kg.
Having already served a two-year doping ban, he could now face a lifetime ban.
"There is no final decision on sanctions relating to the Rio Olympics yet," the International Weightlifting Federation (IWF) said in a statement.
The IWF has declined to make any further comment until the case is closed, but the officially endorsed World Weightlifting magazine has promoted fourth-placed Denis Ulanov from Kazakhstan to the bronze medal and lists Sincraian as disqualified.
Norwegian three-time Olympic cross-country skiing medallist Therese Johaug has also failed a doping test for the prohibited steroid clostebol.
Her country's ski federation said the substance had been in dcame from a sun lotion given to her by team doctor Fredrik Bendiksen, who has resigned and described the violation as his "personal mistake as a doctor".
The England and Wales Cricket Board has defended its disciplinary process following a case involving Somerset bowler Craig Overton.
[NEXT_CONCEPT]
This year's Christmas special episode of Doctor Who, will see the Doctor teaming up with a superhero.
[NEXT_CONCEPT]
A forgotten part of Alexandra Palace could be given a new lease of life if plans are approved to transform a Victorian theatre into a new film, play and concert venue.
[NEXT_CONCEPT]
Romanian Olympic weightlifting bronze medallist Gabriel Sincraian has tested positive for the banned substance testosterone.