Mr Jones said some progress had been made on giving the Welsh Government a greater role in upcoming Brexit talks but there was "no formal agreement as yet".
The Commission, the EU's executive, has started to exclude Britain and its companies from sensitive future work on Galileo ahead of the country's exit from the bloc in a year's time.
A June summit of European Union leaders is the "ultimate deadline" to make progress on issues related to Northern Ireland's border, French Foreign Minister Jean-Yves Le Drian said on Sunday.
Mr Barnier said there had been "misunderstandings" in the coverage of the story, adding: "We are not kicking the United Kingdom out of Galileo".
He said: "It's vitally important for them to be able to keep us and Scotland on board. That clearly is going to cause difficulties for them", he said.
"Barnier (the EU's chief Brexit negotiator) was more pessimistic than I have ever heard him be".
Downing Street has proposed two options in terms of customs - a "highly streamlined" customs arrangement known as "max-fac" - and a customs partnership.
Miliband says the United Kingdom should stay in the European Economic Area, made up of the EU and countries such as Norway that have access to the bloc's single market.
"I think nobody must underestimate the key rendezvous of June", France's Barnier told a security conference in Brussels.
On the British side, former Foreign Secretary David Miliband has joined with politicians from rival parties to call for Britain to retain the closest possible ties with the European Union after Brexit.
"I just can't see how it works if there are no checks on the border between Northern Ireland and the Republic of Ireland and no checks on goods travelling from Northern Ireland to Great Britain, which itself raises a number of political questions that are hard to resolve".