Two people believed to be Muslims praying on an MBTA platform triggered a rapid response from heavily armed transit cops yesterday morning and immediately sparked a debate about when “see something, say something” vigilance can infringe on religious freedoms.

“It’s really up to the person who makes the initial report to make a report based on actual evidence and an actual suspicion and not on prejudice and stereotyping,” said Ibrahim Hooper, spokesman for the Council on American-Islamic Relations, a Washington D.C.-based Muslim civil rights and advocacy organization.

“Too often what we see is that somebody praying or somebody wearing Islamic attire is enough to trigger this kind of response,” Hooper told the Herald. “Often the problem begins with the ?initial report.”

MBTA Police responding to a report of suspicious activity at Wellington Station in Medford temporarily delayed the rush-hour commute into Boston as officers confirmed that the people who prompted the call were not a threat to passengers, MBTA General Manager Frank DePaola said yesterday during an appearance on Boston Herald Radio’s “Morning Meeting” program.

“Some people riding our system noticed two people that appeared to be Middle Eastern, and in their opinion, they were acting suspicious,” DePaola said. “We responded because we got the call. It turns out that they were two citizens lawfully — as I understand it, they may have been praying, because it’s Ramadan.”

DePaola said he hoped the “general misunderstanding” was “resolved in a very gentle manner” and pointed out the incident highlighted a “heightened sensitivity on everybody’s part” in the wake of the horrific mass shooting at an Orlando nightclub Sunday carried out by an ISIS-inspired terrorist who was gunned down by police after killing 49 people and wounding scores ?of others.

And though he said this kind of apparent stereotyping is what often leads Muslims toward radicalization, Northeastern University professor and terrorism expert Max Abrahms said yesterday’s “suspicious activity” report is not unusual given the current climate in the U.S.

“Given all the dangers — both in the United States and abroad — the state department warning Americans not to travel to Europe and the fact that the lion’s share of these attacks are being carried out by the Islamic State or Islamic State-inspired people, observers who are going to be on the lookout for possible terrorist plots are going to make mistakes about who is a real threat and who is not,” Abrahms said.

The call, which briefly delayed commuters, was described by transit police Superintendent Richard Sullivan as a “non-event.”

Sullivan said the officers responded with long rifles they have carried “for years.”

Despite the apparent misunderstanding, Hooper said CAIR will be probing the agency’s response.

“Our Massachusetts office will be reaching out to the transit police to see what happened and to clarify to make sure that all proper procedures were followed,” Hooper said.

“Hopefully there was some attempt to ensure that this kind of incident isn’t purely the result of prejudice and stereotyping … Praying should not be regarded as suspicious.”