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 10 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."
- Sports & Recreation
- Ishmael Miller
- Lukas Jutkiewicz
- Alex Baptiste