Second-half goals from Lukas Jutkiewicz and Zat Knight inspired Bolton to a share of the spoils after Ishmael Miller and Kevin Dawson had put Yeovil 2-0 up at Huish Park.
The Trotters played the last 10 minutes with 10 men after Alex Baptiste was sent off but Miller missed the resulting penalty and Knight grabbed the leveller just two minutes later.
Freedman was full of praise for his side's second-half display and felt Bolton could have even gone on to claim all three points.
He said: "In the first ten minutes we started well and had a couple of half chances but didn't take them. Yeovil then got a foothold in the game and deservedly went 2-0 up.
"Half-time came at a good time for us and we had some strong words and tactically changed the team to go more direct.
"In the end I thought the three points could have gone our way and I'm disappointed not to win it.
"Obviously they had a penalty, I've got no complaints about that or the sending off, but when they missed that penalty it was one-and-a-half minutes before we went up the other end to score.
"We had enough chances to win the football match.
"We've now got a huge week ahead. Our performance has been good at the Reebok and we've got two local derbies coming up."
Yeovil boss Gary Johnson admitted the match "felt like a defeat".
He said: "It does feel like that but we've played a team who were one of the favourites for promotion this year, even if Bolton are struggling in the league.
"We were magnificent in the first half and it feels like a defeat for all of us - supporters, players and the management - because of the nature of being 2-0 up.
"We didn't come out well after half-time. We got the players out early for the second half but Bolton got an early goal which gave them the impetus and we then had to defend.
"We put ourselves in a great position to go 3-1 up with five minutes left but missed the penalty, so with it still at 2-1, it gave them the momentum to have a go and they did.
"I think Marek [Stech] made a bit of a mistake by coming flying out, but unfortunately their biggest bloke got a touch and it went in for 2-2.
"We're disappointed but looking at some of the other results, it could be a point gained, but also two points lost."