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Glasgow 2014 chiefs apologised for delays and difficulties as sports fans attempted to snap up the latest release of tickets which include all 17 sports and the opening and closing ceremonies.
Organisers said they had received reports from some customers of errors in the ticket selection and purchase process.
The ticketing website was closed for one hour from midnight, and bosses said this morning everything seemed to be working effectively.
But this afternoon, people are still tweeting about hours spent in the online queue, and many are complaining they've been kicked out once they have tickets in their basket and are about to pay.
Hear from Chief Executive David Grevemberg here.
Sports fans who previously missed out on tickets and any last-minute buyers were given a chance to secure seats for this summer's event from 10am yesterday on a first come, first served basis.
The 100,000 extra tickets became available as the final arrangements for venue layouts and spectator seating are made, Games chiefs said.
About 2.3 million applications were made for the initial one million tickets released last year, with athletics, aquatics and cycling proving the hottest tickets.
The Queen's Baton touched down on the British Isles on Sunday, arriving in Jersey 10 weeks before the Games begin on July 23.
Over the next 32 days it will travel through Jersey, Guernsey, the Isle of Man, Northern Ireland, Wales and England, before beginning a 40-day journey through 400 Scottish communities on June 14.
Ticket prices start from £15 and are available online via the Glasgow 2014 Ticketing website tickets.glasgow2014.com or the Glasgow 2014 Ticket Hotline 0844 826 2014.
A statement on the Commonwealth Games website said: "As traffic has increased, we have seen some recurrence of issues people were having with the ticketing website.
"We are continuing to sell tickets, but at the same time we need to investigate the cause of these issues and monitor the queue closely.
"We will provide an update on this website and our social channels on a regular basis.''