
Isaac Sinclair opened the scoring for the home side, before second half goals from Craig Carney and Robert Apter ensured that the Lancashire side held on for the win.
Reacting to the defeat, joint-manager Lee Bullock admitted that whilst the result was disappointing, Whitby need to take the positives from the performanace.
He said: "We were on the wrong end of a 3-0 defeat but I don't think we deserved it. The first half could have gone either way and we created more chances than we have in any game recently.
"I said to the lads that our problem is being too easy to score against. The first goal was from a set-piece where no one picked the runner up. The second came from a weak header which has allowed them to get the ball back and whip it in, and the third one was uncharacteristic of Shane (Bland)."
In addition, Bullock took heart from what he saw in the first 45 minutes from his side. "We enjoyed watching it," he said. "We looked good on the counter attack - we were powerful and quick."
Town went into the fixture against Bamber Bridge in poor form, losing 3-1 to Stafford Rangers in their previous league outing.
However, their hosts also entered the fixture out of sorts having lost to lowly Ashton United, and then going out of the Buildbase FA Trophy on penalties against Dunston at the weekend.
Whitby's struggles this season have been when falling behind which is what made the first half even more frustrating given the chances the Blues had.
"When we get 1-0 up we're really hard to beat," said the Seasiders' joint-boss. "We've only come from behind to win once and that was at Mickleover, everything else we've done has been when we've got the first goal."
Bullock outlined the issues his side are facing. "Getting the first goal gives you something to hang on to," he added. "When we go one down we seem to switch off mentally, there are too many gaps appearing because we're not getting back quickly enough."
Looking ahead, Whitby Town's next fixture is on Saturday, when they face Matlock Town in the league.
With a quick turnaround and another difficult game in store, Bullock explained there is no time to dwell on Tuesday night's result and feels that the younger players currently in the squad need to improve and understand the level of football more for this fixture.
He said: "We need to re-group and see what we've got. We've got a lot of young lads involved at the minute and on Tuesday young Harry (Green) was exciting.
"We got to stand up and be counted - it doesn't get any easier after that with FC United. We're in a tough spell at the minute but we will stick together and get through it."