Steve Burr had no complaints about the end result after his side's 2-0 defeat at home to Torquay United.
Chester went into the game in high spirits after the 1-0 win over Macclesfield Town but second-half goals from Aaron Downes and Ryan Bowman gave the in-form Gulls the points.
Torquay keeper Martin Rice made one save, a routine catch from a deflected Jadan Hall shot, as the hosts struggled to create openings.
Referee Karl Evans made a series of strange calls, most notably on 29 minutes when he showed Kieran Charnock a second yellow for fouling Bowman, even though Michael Kay had been the transgressor.
Evans corrected his mistake, booking Kay and allowing Charnock to remain on the pitch.
Burr said after the game: "The overriding thoughts are that we've come up against a side that I think is the best side we've played this season and I know we've been beat by Barnet here, who were a good side.
"I thought in spells we did okay but we just fell short and as I say you've just got to hold your hands up sometimes and the better side won."
Burr admitted Mr Evans' performance left him confused, particularly the decision involving Charnock and Kay, but did not feel it was a factor in the game.
"I was probably the same as everybody else in the ground," said the manager.
"I think the players changed his mind and I don't think the linesman knew. It was bizarre and I was just glad to see that we carried on with 11 players on the park.
"I thought he maybe just lost control of it a little bit for both sides."
Craig Mahon, Callum Morris and Wayne Riley came off the bench during the second half but the changes failed to alter the game.
Burr said: "We didn't feel there was maybe much coming from the middle of the park in terms of creating things but again the opposition were good.
"We brought Wayne on to give us another dimension and give us a bit more pace on the right hand side but it didn't work.
"It gives them lads an opportunity to come on but with the overall effort and commitment we've seen on Tuesday and what we took from Saturday there are things that I'm pleased about that we are improving."
Blues forward Craig Hobson clashed with Angus MacDonald near the end of the first half and again on full-time.
Burr confirmed after the game Hobson had been angry because he believed the Torquay defender had spat at him, although the officials did not act.
"I didn't see the incident but Angus MacDonald I believe has spat in his face but I didn't see that," said Burr.
"You don't get incensed like that for no reason. It's disappointing because you don't really expect that but I'm sure Chris (Hargreaves, Torquay United manager) will deal with it at his end but it's disappointing."
