At least one trip to Pakistan by New York-area bombing suspect Ahmad Khan Rahami raised a red flag when he returned to the United States, prompting border officials to alert the FBI, Fox News has learned.

A Department of Homeland Security official confirmed to Fox News Friday that Rahami was questioned by U.S. Customs and Border Protection agents in March of 2014 upon his return to the U.S. from a 13-month trip to Pakistan. The FBI was notified about the interview months before Rahami's father told the FBI his son could be involved with terrorism.

The FBI told FoxNews.com earlier this week Rahami's father, Mohammad Rahami, later recanted the remark and that investigators had no basis for pursuing an investigation.

rahami journal 921J

A page from Rahami's journal,recovered at the location of his arrest on Monday.

Typically, when someone is flagged like Rahami was, they are given a secondary interview and questioned further. That information obtained from Rahami’s interviews was passed on to the FBI, according to the DHS official.

The information was likely sent to the FBI after being gathered by the National Targeting Center, a division of Customs and Border Protection that targets people and goods at all major ports of entry that pose potential risk to the United States. The NTC is credited with capturing failed Times Square bomber Faisal Shahzad in 2010 as he was boarding a flight to Dubai from JFK.

It is not known what about Rahami might have raised a red flag, but the agency does track individuals who travel to parts of the world where ISIS or Al Qaeda are active.

Questions have been raised as to why there was no apparent follow-up by either DHS, which oversees Border Protection, while the FBI is part of the Department of Justice.

"What happened here, as was the case with other terrorists who came on the governments radar, like Syed Farook, Tamerlan Tsarnaev and others, is that our immigration system is producing alerts, and providing the opportunity to investigate suspicious people and activity, but the leads are not followed,” Jessica Vaughan, director of policy research for Center for Immigration Studies told FoxNews.com. “This is partly because our loosely-run immigration policy has flooded the works with too many people to monitor, and too many immigrant enclaves in which bad actors can melt into the background.”

Ahmad Khan Rahami

Vaughan adds that the current system perhaps enabled Rahami to fly under the radar.

“I believe this oversight on the part of the FBI also stems from a policy emanating from the top that denies any connection between our immigration policy and these incidents of terror attacks, and therefore tends to dismiss or underutilize the national security value of immigration tools,” she said.

Rahami, who has family in Afghanistan and married a woman from the region, made at least four trips to the area between 2005 and 2014, according to the The New York Times.

Other reports surfaced on Friday, which explains what the suspect may have been doing during one of his trips to Pakistan.

Rahami allegedly spent time in a religious seminary in Pakistan that was known to have ties to the Taliban, according to the UK newspaper the Guardian.

Government officials told the paper that Rahami spent three weeks in 2011 at the he Kaan Kuwa Naqshbandi madrassa in Kuchlak, a long-known hub for the Taliban insurgency. The official also said that Rahami also visited other sensitive areas, including Nushki, where former Taliban leader Mullah Akhtar Mansoor was killed during a U.S.-led drone strike.

Fox News Channel’s Bryan Llenas and FoxNews.com’s Malia Zimmerman and Perry Chiaramonte contributed to this story.