The club has fined the pair for the incident, which happened prior to Tuesday evening's defeat by Brentford.
"I'd like to apologise to the Bolton fans for what we did before the game," Trotter, 27, told BBC Radio Manchester.
"We didn't realise it was live, it wasn't aimed at the fans or club, it was a silly gesture as we walked in."
A club statement said: "Bolton Wanderers takes the conduct of its players and staff extremely seriously and will not tolerate such behaviour."
The defeat, Bolton's 22nd in the Championship this season, means they could be relegated to League One on Saturday when they face Derby County.
The club have spent much of the season fighting a relegation battle, as well as off-the-field financial problems, and are 17 points adrift of safety at the bottom of the table with six games left to play.
"It's too hard to pinpoint one thing, there's a lot of things gone wrong. If we knew what the problem was then we would be doing better," said Trotter.
"There's a lot of factors, a lot of outside influence with what's been going on at the club, but it's not just that, the players haven't been good enough this season.
"We haven't done enough on the pitch. We're in the position we're in because we deserve to be."

City had led 2-0 from the first leg after their European debut on Thursday.
Defenders Jennifer Beattie and Lucy Bronze fired in from first-half corners to extend the new English champions' lead, as they controlled possession.
Beattie headed in her second after the break, before Isobel Christiansen slotted in City's fourth late on.
Nick Cushing's side have now kept 19 clean sheets in 24 matches in all competitions so far in 2016.
Scotland centre-back Beattie opened the scoring with a low volley from a right-wing corner on 23 minutes and rose unmarked to head in from another right-wing cross after the break.
Striker Jane Ross had also clipped the inside of the post before Bronze - who netted in stoppage time at the end of the first leg - had drilled home from close range before half-time.
Christiansen's neat fourth added to the margin of victory, after Zvezda striker Daryna Apanaschenko had struck the crossbar with their best effort of a one-sided tie.
Zvezda - who reached the last-16 stage in both of the past two seasons and finished second in the Russian league in September - had not lost a home Champions League match since 2009.
Manchester City Women: Bardsley, Bronze (Corboz 77), Stokes, Beattie, Houghton (c), Asllani (Middag 53), Scott, Duggan, Christiansen, Ross, Walsh.
Subs not used: Hourihan, Parris.
Zvezda: Zvarich, Kurochkina, Pozdeeva, Pantyukhina, Orlov,  Apanaschenko (c), Makarenko, Andrushchak, Nurgalieva, Kipyatkova.
Referee: Riem Hussein
Attendance: TBC

The fee for the 19-year-old will be decided by a tribunal, with Liverpool expected to pay around £3m.
Solanke, who is currently part of England's squad at the under-20 World Cup in South Korea, spent the 2015-16 season on loan at Vitesse Arnhem, scoring seven goals in 25 games.
He made one senior Chelsea appearance.
As Solanke is older than 17 and will sign a professional contract, Liverpool's transfer embargo, which is enforced on signing academy players from other England clubs for two years, will not apply.
Celtic were also understood to be interested in Solanke, whose only Chelsea game came as a substitute in a Champions League victory against NK Maribor in October 2014.
Solanke will officially become a Liverpool player on 1 July.
Find all the latest football transfers on our dedicated page.
Bolton Wanderers midfielder Liam Trotter has apologised for making an offensive gesture with David Wheater in a pre-match live club broadcast.
[NEXT_CONCEPT]
Manchester City reached the last 16 of the Women's Champions League as a 4-0 victory in Russia sealed a dominant, 6-0 aggregate win over Zvezda 2005.
[NEXT_CONCEPT]
Liverpool are to sign Chelsea's teenage forward Dominic Solanke after he failed to agree a contract with the Premier League champions.