Because of the changes, which went live Aug. 1, students have had trouble logging into the system and making credit card payments and have experienced delays in submitting their applications. Colleges, meanwhile, have had trouble uploading the applications and have had to manually check the material.
"Technology is a wonderful thing except when it isn't," said Marjorie Neff, principal of Masterman, one of the city's top magnet high schools, where virtually all students go to college. "It's making me anxious, thinking about how we're going to ensure the information has gotten to the universities like it was supposed to."
Kathleen Dopkin, dean of the high school, said she helped one of her students get onto the system and then hit the submit button to send the application. She then asked to preview the information she had just submitted, and it gave her an application for a different Masterman student, she said.
"Getting on the system and staying on the system has been very difficult," she said. "It has randomly lost information."
The Common Application, a nonprofit company that administers the system, has acknowledged the problems and is working to fix them.
"On Wednesday, we released an update to fix two of the issues that some users were facing," spokesperson Aba G. Blankson said in an e-mail. "Since then, we have seen marked improvements."
Richard DiFeliciantonio, vice president of enrollment at Ursinus College in Collegeville, said he noticed improvements on Friday. The college had 200 applications in its queue unable to be uploaded and read.
"Today, the data came flowing through," he said.
DiFeliciantonio said the college had been considering printing out applications and sending them to students.
"It was causing us a little bit of anxiety," he said.
Not all local schools use the common application. Pennsylvania State University and Rutgers University, for example, do not.
Princeton, which had used the common application exclusively, announced earlier this month it would give students another option because of the problems.
"We decided to provide them with the option of using the universal college application beginning Oct. 10," said spokesman Martin Mbugua.
At Drexel University, about 28,000 of the school's 43,000 applications last year came through the common application process. Enrollment officials there are trying to weather the problems by "putting a lot of Band-Aids on the system," said Erin Finn, assistant vice president of admissions.
Instead of automatically uploading forms, the staff has had to do some of the work manually, she said. They are printing out forms and then scanning them into students' electronic files, she said.
"We're getting really concerned that we won't be able to maintain our Band-Aid process as our volume increases. So we're sweating this one," she said.
The school's deadline for early action is Nov. 1.
"We have concerns about the integrity of the data," she said, noting that the staff had discovered discrepancies in answers to critical questions like: "Do you have a disciplinary record?"
Finn said staff had been assuring concerned students the problems would be worked out. She encourages students to reach out to the universities to which they applied and monitor their application "portal" on each university's website.
"They really need to understand the status of their application as it relates to each individual school," she said.
Finn said the company never should have rolled out the system this year. It clearly wasn't ready, she said.
"They should have beta tested it and just stuck with the version they used last year for this year," said Jim Yannopoulos, a Bryn Mawr educational consultant.
He said high schools that use Naviance, a college search site that meshes with the common application and allows counselors and teachers to send transcripts and recommendations, had been hit particularly hard because of the problems. In some cases, teachers and counselors have been unable to get the materials to go through.
Yannopoulos' concerns weren't alleviated upon hearing that the company had fixed some of the problems.
"It looks like a Whack-a-Mole," he said. "Something else pops up and they try to figure out a fix. You get the feeling that they don't even know what the underlying problems are."
Gaynor, Villanova's admission director, gave the company points for trying.
"To their credit," he said, "they've owned it and they're trying to fix it."