The Scottish Premiership club have announced that the pair "have agreed the termination of their loan period at Rugby Park by mutual consent".
Defender Waddington and goalkeeper Davies were two of 11 players signed on one day by Killie manager Lee Clark.
Both made two appearances for the Scottish Premiership club.
The 19-year-old Waddington made one start, against Greenock Morton in the Challenge Cup and a substitute appearance away to Hamilton Academical in the Premiership.
Davies, who is two years older and was on his second loan spell at Rugby Park, played against Berwick Rangers and Albion Rovers in the Challenge Cup.

Marjory Stewart, of Bellshill, Lanarkshire, is alleged to have crashed into three other vehicles during the incident in Portsoy in July.
She is accused of failing to keep her car under proper control.
The case called at Banff Sheriff Court and was continued without plea until next month.

Paul Mason, of Ipswich, used to weigh 70 stone (440kg) but has lost more than 40 stone (254kg) with the help of gastric band surgery.
He hopes the procedures in New York will help shed seven stone (44kg). His visa application had been delayed due to a previous criminal conviction.
Mr Mason still needs to raise about Â£7,000 towards surgery-related costs.
He was in the US in December for a consultation with Dr Jennifer Capla, who offered to remove his excess skin for free after hearing that the NHS would not perform the operations as quickly as Mr Mason hoped.
However, his plans to make a quick return to the country were delayed when his visa application was referred to Homeland Security in March, because of a conviction for fraud in 1986.
He has now received his visa and had been due to have surgery on 20 October.
But this has been postponed as he needs to raise $12,000 (Â£7,400) to cover the post-surgery costs, which include accommodation and medicine. He is due to fly out later this week.
Last time he was in the US he appeared on The View TV programme, where he accepted a marriage proposal from his girlfriend, Rebecca Mountain, who lives in Massachusetts.

He said it was "dispiriting if pretty unsurprising" to see David Cameron's government turn their back on the coalition's "liberal stance".
The former deputy prime minister also criticised his former partners' "swagger" over the EU referendum.
And, in his final speech to MPs as Lib Dem leader, he predicted the EU debate would "devour" Mr Cameron's party.
A contest to replace Mr Clegg is under way after the election left his party with just eight MPs.
"My party's presence may be much, much reduced in size, but our mission is clearer than ever," said Mr Clegg.
He said new data monitoring powers, resisted by his party in government, represented a "turbo charged snooper's charter", and said there had not been enough to support social care and house-building.
He accused the Conservatives of ditching their commitment to civil liberties.
"The human rights we hold dear, our right to privacy in an online age, our future as an open-minded, outward-looking country, are all hanging in the balance again because of the measures announced today," he said.
"The previous coalition government's commitment to fairness is weakened," he added.
Mr Clegg said he sensed "a slight swagger" among the Conservatives over Mr Cameron's bid to repatriate powers from the EU, saying the PM was "ambivalent" towards the UK's place in Europe.
And he called for electoral reform and wholesale changes to Britain's constitution, adding: "This sort of piecemeal tinkering does not go nearly far enough."
He began his speech, in a half empty chamber, by saying it was "an unaccustomed surprise" to speak in the Commons without being greeted by a "disobliging wall of noise" from the opposition benches.
Following the Lib Dem leader in the Commons, Conservative MP Andrew Mitchell said history would treat Mr Clegg's time as deputy prime minister more kindly than the electorate had.
Stoke City's Mark Waddington and Swansea City's Oliver Davies have had their loan spells with Kilmarnock cut short and returned to their clubs.
[NEXT_CONCEPT]
An 81-year-old woman is due in court charged with injuring four people - one seriously - while driving dangerously in an Aberdeenshire village.
[NEXT_CONCEPT]
A man once dubbed the world's fattest has been granted an American visa so he can have surgery to remove excess skin.
[NEXT_CONCEPT]
Nick Clegg has accused the new Tory government of abandoning the values he said had been at the coalition's core.