Despite leading 2-1 when Danny Rowe blasted the National League club in front, Will Grigg was on fire and Wigan ran out 3-2 winners.
But there were no regrets for the Coasters manager even though he knew on another day it could have been his team going through to round three.
He said: “You have to be disappointed but filled with an enormous amount of pride at the same time.
“Regardless of what happens in these games, you have to use them as learning experiences. We have to use this as motivation, not just for us ourselves this season in terms of what we can achieve but ultimately for the players as individuals.
“They can go and achieve what they want. Their ambitions should be to go and play on that stage every week.
“There is only one person who can stop them and that is themselves. That is what they have got to do – be proud of what they have done. It is the furthest this club has ever been in the competition, and this season’s league position will be the highest this club has ever been.
“We have to use this as motivation to really kick on and do something special this season. We will save the third round for next season.”