A typical performance from the Latics who dominated possession but lacked a cutting edge, finally relenting to a set-piece in the final moments of the game.
The arrivals of Victor Moses and Marcelo Moreno are more than needed to give a much needed threat.
Here is the reaction of the two managers.
Roberto Martinez
It is a difficult result to take but it's not the first, and it won't be the last time we're tested. We knew the first goal was going to be important and I thought we created some good open opportunities. But we failed to take them, and when that happens you run the risk of being defeated, which is exactly what happened.
We made a few changes today but there are a lot of games coming up, so it's important to use your full squad, and for certain players it was important to be out on the pitch playing and getting game-time.
We have to congratulate Notts County, they approached the game with huge determination, huge fight and got everyone behind the ball when they had to. We did well to open them up and create chances but if you don't convert them you don't win football matches.
It was a chance at a good cup-run but it probably came at the wrong time for us in a season where things have been difficult. Probably now we're just starting to get a settled side after many ins and outs and we have to focus our attentions on the league now.
It's paramount that our league form is our main priority, the FA Cup, as nice as it would have been to go on a good run, was probably a distraction we could have done without at this stage.
But I guarantee that we'll react in the right way and make sure we put this disappointment behind us very quickly.
It's important that we all understand where we're going wrong, what needs addressing and what lessons there are to be learned from the last three games.
We all understand the disappointment the fans are feeling, but now is the time we all need to pull together as a football club and make sure that we react in the right way on Saturday.
We're going to have a lot of games to play this month and we have to focus now on getting the points our performances deserve. Today was a big blow but I think it will present a big test in character in the dressing room and we'll approach it in the right manner.
Dave Kevan
I'm just trying to get on with things and keep the lads focused. Thankfully I've been able to do that because they're a great bunch.
It's been a very enjoyable evening. Wigan put us under a lot of pressure but we held on and did very well.
It's a very tough game we've got in prospect (at Fulham). They're a top side, just like Wigan are. But we'll go there and and see what happens.
We approach every game the same and we make sure we do the right preparations. That's exactly what happened.
Lee Hughes and Kasper Schmeichel have put on a top performance, just like all the other lads but they won't be fazed by going to Fulham.
Next game
A trip to see Steve Bruce in Sunderland awaits the Latics on Saturday. Hopefully Moses and Moreno will be available for this one.