Jones said: "I think that's why we're not top eight and pushing for top six at the minute as we've missed opportunities.
"Both Swansea games, both Middlesbrough games, Birmingham here, (Nottingham) Forest here, there's a lot of ones where we should have taken more and we should have a greater points haul and be closer to those who are challenging for play-offs.
"But it's another point, a point against Middlesbrough, we're kind of saying we should be beating these sides, so we've come a long way and let's not forget that, but I'm disappointed today as we should have taken three points.
"For large parts of the first period we were really lacklustre, we didn't really get going.
"Second half we picked it up and we had enough of the play, enough of the opportunities, we just need to show a little bit more control and quality and we probably would have won the game."
The official did then give a spot-kick when Paddy McNair was adjudged to have tripped Kiernan Dewsbury-Hall, only for Collins to see his effort repelled.
Pelly-Ruddock Mpanzu also hammered over from the resulting corner.
Boro boss Neil Warnock said: "It was two honest sides both giving everything they've got and I thought we deserved that.
"I thought we were a bit unfortunate when Sav's shot hit their man, I thought that would have gone in, but you've got to take your hat off.
"Nathan's got a real honest, hard-working side and I think we had to work hard to get that result.
"It was a good move for the goal, Duncan's been lively and I feel a bit sorry for him as he's had to do a little bit more work today with the system they play, but overall I thought he put another good shift in.
"I don't think it was a penalty, he's slipped hasn't he? You can see can't you, there's no contact with the man.
"I think he gave that as he probably thought the first one might have been a penalty, so I think that would have influenced him, or he just doesn't like Paddy as he sent Paddy off last time against Huddersfield and we got that card rescinded.
"So I've just said to Paddy, it must be just you he doesn't like."