A message popped up telling shoppers that they should wait roughly 10 seconds, then refresh their browser, to enter the site. Once the page was reloaded, however, another glitch prevented some customers from adding items to their carts.

The issues came up on what is seen being one of the largest days of the year for online sales. Digital revenues are expected to rise 11.3 percent on Black Friday to $3.05 billion, according to Adobe Digital Insights.

The flub is the latest in a series of issues on bricks-and-mortar retailers' websites. Last year, Target suffered a high-profile slowdown that prevented shoppers from checking out; the year before, Best Buy had issues.

ChannelAdvisor has previously said that retailers lose about 4 percent of a day's sales each hour their sites are down.

"We are currently experiencing high volume on our site, which has slowed traffic," a spokeswoman for Macy's told CNBC. "We are still taking a high volume of online orders, and we are working quickly to alleviate the delay issue which we hope to have resolved shortly."

The company's Black Friday deals are available through midnight on Saturday, the spokeswoman noted.

On Thursday, Macy's reported a strong start to the Black Friday weekend, with 16,000 people rushing into its Herald Square New York flagship at the open at 5 p.m.

Catchpoint Systems, which monitors retailers' web performance, also reported slow load times on Williams-Sonoma's page, of more than 25 seconds. Spokespersons for that brand did not immediately respond to CNBC.