Newport County were forced into a late team reshuffle at Sincil Bank and suffered the consequences.
Defender Mark O’Brien cried off with illness just before kick-off, County changed their team shape to accommodate late call-up midfield player Matty Dolan.
“Pipey was out with a hamstring injury and O’Brien was sick after we’d put the team sheet in but it is what it is,” said Flynn.
“I’m not making excuses, we defended poorly.”
“We conceded three sloppy goals and you can’t do that, that’s the bottom line.”
Newport suffered their first defeat of 2018, but Flynn insisted the loss had nothing to do with their FA Cup clash with Spurs.
His players have a Wembley Stadium replay date with Tottenham in the FA Cup, but Flynn will insist they focus on Colchester United away this Saturday.
That League Two clash is crucial to County hopes of maintaining their push to finish in the play-offs.
“There was no cup no hangover,” said Flynn. “We played some really good stuff and the players worked and worked and worked.
“They kept going to the end and we nearly scored again at the end but our defending was not good enough.”
“Whether you’re the freshest team in the league or the most tired team, if you give away three goals like we did then you’re going to lose.
“The boys put in an unbelievable effort. Lincoln are strong at what they do and you can’t give away goals like we did, so that was the disappointing thing.
“We created chances but we conceded a free header in the six-yard box to their 6ft 4ins striker. It’s not as if you can miss him.”
The big moment of this match at Sincil Bank came just before half-time with the score at 1-1.
Padraig Amond had already scored and almost scored his second when he beat Lincoln’s offside trap with a perfectly timed run. Goalkeeper Paul Farman reacted fast, narrowed the angle and saved with a leg.
Amond netted his 11th goal of the season, while Matt Rhead, Matt Green and substitute Ollie Palmer netted for Lincoln.
David Pipe was ruled out by injury, while O’Brien pulled out because of sickness.
Flynn’s reshuffle saw Dolan slot into midfield alongside Scot Bennett and Joss Labadie with Ben Tozer playing at centre-back in a 4-3-3 system. Ben White moved to full-back.
Lincoln jumped above County, who are now 10th in League Two, three points outside the play-offs.
Big striker Rhead was allowed a free header from three yards to scored Lincoln’s first from a Green cross after 14 minutes.
Amond equalised just after the half hour, cooly sliding his shot home after Dolan’s shot had been parried.
Green volleyed Lincoln’s second from Rhead’s pass, while Palmer’s shot from 25 yards went in off a post less than a minute after he had gone on from the bench.
The defeat was a major blow for County, who now need a big performance at Colchester on Saturday.
Newport: Day, White, Demetriou (Sheehan 80), Bennett, Butler, Willmott, Dolan, Tozer, Labadie (capt), Amond (Hayes 80), Nouble (McCoulsky 66). Subs not used: Bittner, Collins, Reid, Osadebe,
Lincoln: Farman, Habergham, Waterfall (capt), Bostwick, Eardley, Anderson, Woodyard, Frecklington, Rowe (Williams 78), Green (Palmer 72), Rhead (Wilson 60). Subs not used: Walton, Long, Whitehouse, Stewart
Referee: Scott Oldham
Attendance: 7,567 (76 away).
