Several hundred, including young children and babies, spent the night in the open at Croatia’s border with Slovenia.
The UN refugee agency (UNHCR) also complained of a lack of basic supplies at the Serbia-Croatia border.
The western Balkan route has been disrupted by government restrictions.
Hundreds of thousands of refugees, many from Syria, Africa and Afghanistan, have been making their way from Turkey to the Balkans in recent months, in a bid to reach Germany, Sweden and other EU states.
Slovenia decided at the weekend to restrict the numbers crossing its territory in response to what it said was Austria’s new policy of cutting the numbers entering – something Austria denies.
More than 10,000 refugees are now stranded in Serbia, barred from entering Croatia, according the UNHCR.
“There is a lack of food, lack of blankets – we are missing everything,” spokeswoman Melita Sunjic told Reuters.
On the Croatia-Slovenia border, 500 people spent the night in the open at Trnovec. Police have now allowed them to shelter under canopies attached to immigration huts.
A further 1,800-2,000 slept on a train held on the Croatian side of the border.
Officials told them they could stay temporarily in Croatia or try to make their own way into Slovenia.
Croatia had asked its northern neighbor Slovenia to accept 5,000 refugees daily, but Slovenia said it would only take half that number.
Explaining Slovenia’s new restrictions on October 18, Interior Ministry State Secretary Bostjan Sefic said its northern neighbor Austria was only accepting a maximum of 1,500 people a day.
He said that Slovenia “cannot accept unlimited numbers of migrants if we know that they cannot continue their journey”.
Hungary, citing security concerns, has closed its borders with Serbia and Croatia, forcing refugees to switch to a slower route via Slovenia.
There are reports in Slovenian media that restrictions on its borders with Austria and Croatia are being eased.
Germany’s welcome for Syrian refugees continues to create internal political tensions.
The Pegida organization, which campaigns against immigration, says it expects tens of thousands to demonstrate in the eastern city of Dresden on October 19.
Interior Minister Thomas de Maiziere has described Pegida as “hard-right extremists”.
More than 600,000 people, most of them Syrians, have reached Europe so far this year compared with just over 200,000 for the whole of 2014.
Germany has said it expects 800,000 asylum seekers in 2015, but it is believed the number could be as high as 1.5 million.
Image source: Wikimedia Commons President-elect Donald Trump celebrated his election victory at the Ultimate Fighting…
Millions of voters across the US chose to return Donald Trump to the White House…
Donald Trump declares victory in the US election as he addresses jubilant supporters in Florida.…
Stocks around the world are rising as Donald Trump appears to be on the cusp…
Donald Trump has won Pennsylvania, North Carolina and Georgia and taken a lead over Kamala…
Quincy Jones, the celebrated musician and producer who worked with Michael Jackson, Frank Sinatra, Ray…