The biggest reason retailers struggled to meet online demand this year was a result of the "sea change in the industry," Jones said. In particular, it's the rapid adoption of mobile platforms that threw companies off.
That's because retailers' mobile sites use what's called responsive Web design, a tool that reformats content that's delivered on a mobile device. If a retailer doesn't do a good job making its responsive Web design function exactly the way it should, it can shake the company's technological infrastructure to the core, Jones said.
At Best Buy, the company attributed its crash to "record levels" of traffic, including a "concentrated spike in mobile traffic." The retailer temporarily shuttered its site to restore its performance.
Read MoreNo way Black Friday sales fell 11 percent: Analyst
"Many of these retailers, they're not necessarily configured correctly to deal with that increase in mobile traffic," Jones said. "Ultimately what I think it boils down to is the applications that they manage are just incredibly complex."
According to IBM Digital Analytics Benchmark, this year was the first time when the weekend after Thanksgiving saw mobile traffic account for more than half of all online traffic. That followed an increase in mobile share on both Thanksgiving and Black Friday, as well.
But it isn't just the shift to mobile that's complicating retailers' performance. Wingo said retailers can see their traffic spike between 6 and 10 times what's typical over the Black Friday/Cyber Monday period.
"It is a very hard kind of computer science problem," he said. "How do you prepare for that?"