Biggar was heard on television coverage querying whether to kick for the corner when Wales were awarded a penalty while trailing 16-13 in the 51st minute.
But Leigh Halfpenny has admitted he turned down the chance to kick at goal.
“So as for me over-ruling the captain, where that’s come from I’ve got no idea,” said Biggar.
“It’s been a pretty hurtful couple of days in terms of me being questioned whether I’ve over-ruled the captain, let alone someone I respect as much and has achieved all that Alun Wyn has in the game.”
The incident came in the 51st-minute of the match when Wales were trailing 16-13 and a successful kick would have drawn them level.
Biggar, who has made 54 appearances for Wales, said he had asked Jones about kicking for the corner before turning to give the ball to Halfpenny after Jones had said he wanted to kick for goal.
“Leigh has held his hands up, he said he didn’t fancy the kick then Alun Wyn has said … we’ll go for the corner, and we’ve gone to the corner,” added Biggar.
“In terms of this incident it needs to be put to bed because it’s pretty hurtful when you’ve got people phoning you up and asking if you’ve disrespected your captain or over-ruled your captain.
“That’s the truth of the matter, so maybe it’s a bit of a lesson for everyone.”
Biggar is among the more vocal and outwardly confident players in the Wales team and fells that fact may have influenced the way the incident was reported.
“I think everyone sees a side of me which is quite full of confidence,” he said.
“But ultimately things like that are quite hurtful not only to me but to my family and things it’s not nice for them … to have to read some of the stuff which was said.
“The most important people are the people inside these four walls at the Vale [team headquarters at the Vale of Glamorgan Hotel) and my family and friends and everyone else’s opinion is not at the top of my agenda if the truth be told.
Wales must get better
Biggar said the Wales team – who suffered their first defeat by Scotland since 2007 – did not believe the incident had a major bearing on the outcome of the match.
“We’re not hiding the fact that we spilled a lot of ball at the weekend, we made unforced errors and didn’t put enough pressure on Scotland,” he added.
“For us to say that us making that decision has affected the outcome of the game would be very harsh and unfair.
“Bottom line is we didn’t keep hold of the ball, we didn’t stress Scotland enough and probably got what we deserved in the second half.”
Wales face Ireland next on Friday, 10 March with Biggar acknowledging they need to make a big improvement before that evening kick-off and the match against France on 18 March.
“We’re playing against a top top team in terms of the roll that they’ve been on.
“Obviously they’ve been stunned up in Murrayfield first game of the Six Nations and it turns into a must-win game for them because a defeat will probably put them out of the title race.
“We’ve got two huge games in terms of getting back on the horse and showing more of the performance we showed against second half against Italy and against England.
“We’re a lot better than [we showed] that second half in Murrayfield.”