Earl, who had come on as a substitute at half-time for Paul Huntington, was booked twice in the space of nine minutes and was shown a red card by referee Keith Stroud in the 81st minute.
There is no right of appeal against a red card for two cautions and left-back Earl will miss next Saturday's visit to Queens Park Rangers through a one-match suspension.
Neil said: "The sending-off was extremely harsh, I have seen both tackles back.
"There were worse tackles in the game for both bookings, I don't think either of them were clear bookings.
"Certainly the second one in particular was harsh.
"Josh was pleading his innocence afterwards and I can see why having watched them back.
"We didn't even think the second one was a foul."
Earl's introduction at the interval was his first slice of action since suffering a thigh strain at Birmingham on December 1.
He was introduced to allow Andrew Hughes to move into the centre of defence, Neil not having been happy with the balance in the middle in the first half.
Neil said: "I'm really disappointed for Josh because he has been out injured and this was his first taste of action for a while.
"Then he gets off for something which was really soft.
"It is what it is and we have to get on with it.
"To be honest we have played with 10 men that often this season that we are getting used to it."