The game was settled by two goals in five minutes, a wonderful opener from Randell Williams quickly added to by Dion Charles’ second.
Appleton questioned why the recovered Terrell Thomas was not allowed back on to the field when Charles scored the visitors’ second in the 21st minute.
And even though it is now back-to-back defeats for the first time on his watch, the Addicks manager still took plenty of positives from the second-half effort by his side, even if it didn’t reap rewards.
He said: “Apart from the two goals and the moments, I can’t be too disappointed.
“I’m obviously disappointed to lose 2-0 against a good side but I think looking back at the moments I’ve tried to look back on in the changing rooms there, when it comes to XG and all that we were higher than Bolton.
“Now that might be hard to believe and read, but I could actually believe that because I think sometimes when you find yourself behind in games it’s easy to sort of feel sorry for yourself and step away from it.
“But the way the players sort of reacted in the second-half gives me great confidence going forward.”
Appleton accepted Bolton were the better team in the opening 45 minutes but had big questions about the second goal, not only for Thomas not being allowed back on but also claiming Scott Fraser had been impeded by referee Geoff Eltringham.
The SE7 boss said: “Obviously in the first-half we were a little bit shy of them.
“We weren’t aggressive enough and probably showed them a little too much respect.
“I will take responsibility from that point of view – we can be a little bit more aggressive.
“Having said that, there were moments when I thought the players could have done that a lot more in the first-half.
“But ultimately when you concede the first goal – the first goal was a wonderful goal -but the second one, in the manner that we did, you could feel it within the stadium.
“There was an anxiety about what had happened and that is through no fault of the players because I think it was 38 seconds before the ball actually got back towards that half of the field in that period.
“But the biggest frustration for us more than anything was that Scott Fraser got blocked by the referee, so he couldn’t track the run into the box.
“It was almost like a double-edged sword.
“We were punished for having a player off the pitch and punished then from having a player obstructed by the ref.”
