Swindon sprang an upset on Stoke after extra-time, while Fulham were dumped out by Sheffield Wednesday in the second round of the Capital One Cup.
The 10 other Premier League clubs involved all progressed to the third round, but Blackburn, Bolton and Leicester were among the Championship sides on the end of upsets by lower league opposition.
Stoke City crashed out after they were beaten 4-3 at home to League One high-fliers Swindon after extra-time, with James Collins scoring a hat-trick in a dramatic clash at the Britannia Stadium.
Fulham were another Premier League side to suffer a shock defeat, losing to Championship newcomers Sheffield Wednesday after Gary Madine converted a 50th-minute penalty to hand the Owls a 1-0 win.
Maynor Figueroa scored a wonder-goal for 10-man Wigan as they disposed of Nottingham Forest 4-1 at the DW Stadium. Simon Cox's strike was also a stunner as he pulled one back for the Championship side, while it was the Latics' Antolin Alcaraz that was handed his marching orders for a second booking.
James McClean netted a brace as Sunderland triumphed against League Two visitors Morecambe 2-0 at the Stadium of the Light, with the winger scoring either side of the break.
Fabian Delph, Chris Herd and Darren Bent were on target for Aston Villa as they saw off visiting Tranmere 3-0 to advance to the third round.
West Brom recovered from an early scare against League One leaders Yeovil to triumph 4-2, with Shane Long scoring a double to counter a Reuben Reid brace for the hosts.
Crewe failed to get on the scoresheet on their trip to West Ham as the Premier League side saw off their League One visitors 2-0, with Nicky Maynard and new signing Modibo Maiga finding the back of the net.
Swansea continued their excellent start to the season with a 3-1 victory over Barnsley at the Liberty Stadium, with Luke Moore netting a double.
QPR eased past League One visitors Walsall at Loftus Road after Shaun Wright-Phillips and Bobby Zamora got on the scoresheet either side of half-time before Jose Bosingwa sealed a 3-0 triumph.
Norwich overcame Scunthorpe with a 2-1 win at Carrow Road thanks to a Wes Hoolahan penalty in the second half.
Premier League newcomers Southampton claimed a 4-1 road victory at League One Stevenage, with a last-gasp strike from substitute Ben Reeves sealing the win.
A flurry of early goals saw Reading go behind to Championship visitors Peterborough but a Nathanial Knight-Percival own-goal sealed a 3-2 win for the Premier League new-boys in the 38th minute.
League One newcomers Crawley sprang a 2-1 upset over Bolton after late drama at the Broadfield Stadium saw Nicky Ajose score a crucial winner.
Championship side Leicester suffered humiliation at home to League Two visitors Burton Albion as the lower ranked side secured a 4-2 win.
Blackburn could not build on their Championship win at the weekend as a Luke Chadwick double fired League One MK Dons to a 2-1 success.
Leeds United proved too strong for League Two visitors Oxford United at Elland Road, claiming a 3-0 win thanks to goals from Rodolph Austin, Sam Byram and Tom Lees.
Preston North End were quick starters against Crystal Palace, with a brace from Nicky Wroe, including a second-minute opener, helping to secure a 4-1 triumph at Deepdale.
League Two Gillingham could not continue their bright start to the season at home to Championship visitors Middlesbrough, who won 2-0.
Bradford City snatched a last-gasp strike to upset Championship side Watford with a 2-1 road success, with Garry Thompson grabbing the winner.
Doncaster completed an impressive comeback from two goals down to triumph 3-2 over 10-man Hull City, with David Syers grabbing his second of the night for the winner.
Coventry upset visiting Championship side Birmingham 3-2 after edging out their opponents in extra-time, with Carl Baker grabbing the League One side's winner.
Substitute David Symington fired League One Carlisle past Ipswich after extra-time to dump out the Championship visitors 2-1.
Robbie Williams' stoppage-time spot-kick drew Plymouth level with Burnley at Turf Moor, with the 1-1 scoreline sending the game into extra-time, but it was the Clarets who ultimately prevailed 3-2 on penalties.