Yesterday evening, the BBC website and BBC iPlayer became inaccessible for about an hour from around 8pm.
Sections of the BBC website came back online at around 9.10pm, but throughout the day users reporting that the 'Most Popular' section was flagging old news items.
The BBC has said today that two issues were unrelated, but the outage was caused by a "failure of the traffic managers" in both of its data centres.
It is currently investigating the "root cause" of the incident, which follows a similar hour-long blackout in March 2011, which also attracted criticism from users.
A statement from the BBC said: "Due to a major technical issue, BBC Online was temporarily down on Wednesday evening.
"Service was restored to most users within an hour. We are working on full restoration as quickly as possible, and are investigating the causes of the outage."
Alongside the outage, BBC.co.uk's 'Most Popular' section showed a mix of old and new news stories yesterday, including some dating from June 11, such as "Apple ditches Google Maps in iOS6" and "Camerons left daughter at pub".
BBC News website editor Steve Hermann acknowledged the issue, tweeting: "Working to fix issue of old stories showing in 'Most read' list on @BBCNews site. We're sorry and hope to fix soon."
In a blog post at 11.41am on Wednesday morning, Hermann elaborated: "As some of you may have spotted, there's a problem at the moment with some of the data in our "Most Popular" module, where the "Most Read" section is pulling in some older stories (check the story date stamp if in doubt) along with new ones. We apologise for any confusion this is causing. We're working to fix it as soon as we can."
However, some users turned to online message boards to criticise the BBC for the problems.
In response to Hermann's blog, a user called Sandstorm wrote yesterday evening: "Bad day for BBC on-line (sic) today. The 'Most Popular' is nothing compared to the whole of bbc.co.uk being down for an hour. Parts took longer to return.
"Thank goodness Radio4 (sic) long wave still has a few spare valves left."
Another user called ThinkTank added: "How about sorting out your own problems before expending ANY effort on a story that might get buried by month-old news?
"10 hrs & counting ... Will this attract the level of coverage the BBC gave RBS if it's still unsolved after 3 days? (thought not) Anyone want to resign? (thought not)."
In a blog post this morning, BBC controller of digital distribution, Richard Cooper, confirmed that the site started to fail at 8.10pm, and was completely down by 8.25pm.
Copper said that it started to recover at 9.10pm and then was fully back by 9.30pm, although some users may still have been experiencing issues up to 10.10pm, when all problems were resolved.
"The problem was caused by a failure of the traffic managers in both our data centres," he said.
"These traffic managers are a critical part of our infrastructure, responsible for handling all requests to the site, and routing those requests to the right servers. They are designed to be highly reliable, and have served us very well to date.
"We are still investigating the root cause of this incident, and I would like to apologise for any inconvenience that this outage may have caused.
"We are working hard to make sure that the causes of the issue are addressed, and that this does not happen again."