"Sloppy record-keeping" by the college is likely the cause, Mignott told CNBC. The Morehouse case is still in court and the college denies it's at fault.
Cooper, whose organization spent four years successfully helping 4,500 former students who were nine credits or less away from graduating through its Project Win-Win, said many colleges hobble students by requiring them to opt-in to get the diploma. The extra step—usually paperwork specifically asking for the degree, along with a check—sometimes gets lost in the shuffle and many students assume this step happens automatically.
When her team contacted ex-students saying the Win-Win program wanted to help them finish their degree, some thought it was a scam because they thought they already had their degree.
A full 17 percent of the U.S. population has some college but no degree, Cooper said.
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Financially, the difference between some college and an actual degree adds up over a lifetime, said Jeff Strohl, the director of research at the Georgetown University Center on Education. On average, over a lifetime, the person with an associate's degree will make $200,000 more than someone with "some college." A person with a bachelor's will make $700,000 more over a lifetime than the person who didn't finish a degree, Strohl said.
Strohl also wasn't surprised that Tovar found out too late that he didn't have all the required credits. But it's hard to determine how many other people are in that same boat, compared with the number of people who intended to drop out of college, often due to financial or academic problems. Roughly, he estimated it could be between 4,000 and 20,000 people a year who have not actually graduated from college due to an "oops factor."
Many of those may never know it until a company such as the National Student Clearinghouse, a nonprofit, tries to verify information. On its website, the company claims that "41 percent of applicants lie about education."
Of the 31 million students who enrolled in college within the past two decades but didn't get a degree, 4 million made at least two years of progress, according to a National Student Clearinghouse Research Center report.
"If you go out and help (the almost-grads) during a recessionary economy, those people go from barely making it, to better off," Strohl said. "It makes a difference."
—By CNBC's Amy Langfield
(CORRECTION: National Student Clearinghouse is a nonprofit. It has not urged colleges to track down their students who are just shy of graduation, as was stated in an earlier version of this story.)