Why do Turkish Airlines gate agents at Istanbul Airport take photos of passenger passports?

This happened to me while in transit at Istanbul airport. I asked the guy clicking pictures and he was like it’s required for the airlines (Turkish) by the destination country (Canada) and it was getting done for everyone regardless of nationality. They lined people up when boarding to check handbags (literally opened everything) and whatnot after clearing the security.

The passports of me and my co-travellers were also photographed in Istanbul before entering a plane to Germany last year. I think we were the only people from that flight that got their documents photographed. My assumption was that it was related to the following

• one of my co-travellers had her German residence as a sticker in her passport rather than in the form of a separate plastic card. The boarding gate lady had asked for an “Ausweis” earlier, which probably means that she found this kind of residence permit odd (It actually is somewhat odd, but it is something that the passport holder has little influence on).
• the co-traveller is from a country that is not really known for reliable documentation
• the co-traveller looks as she might be from a country that is a major source of refugees and we were transiting from a country that is just next door

In short, my assumption was that it was related to immigration regulations and financial risk for the airline in case of transporting any undocumented passengers.

Personally I have never experienced what you’ve described when passing through Istanbul, so it is most likely dependent on either the destination of the flight, or the citizenship of the passenger.

Most likely they are doing it because the regulations of the country the flight is going to requires them to do so. For example, Timatic (the system most airlines use to confirm passport/visa requirements) states the following for flights to the Netherlands:

Warning: Airlines flying from the following airports to the
Netherlands: Abu Dhabi (AUH), Accra (ACC), Bahrain (BAH), Beirut
(BEY), Buenos Aires (EZE), Casablanca (CMN), Cartagena (CTG), Damman
(DMM), Dar Es Salaam (DAR), Doha (DOH), Dubai: International Airport
(DXB) or Al Maktoum (DWC), Entebbe (EBB), Freetown (FNA), Guangzhou
(CAN), Hong Kong (HKG), Istanbul: Istanbul (ISL) or Sabiha Gokcen
(SAW), Izmir (ADB), Paramaribo (PBM), Johannesburg (JNB), Kiev (KBP),
Kigali (KGL), Konya (KYA), Kuala Lumpur (KUL), Kuwait (KWI), Lagos
(LOS), Moscow (SVO), Muscat (MCT), Nairobi (NBO), New Delhi (DEL),
Robore (RBO), Sao Paulo (GRU), Singapore (SIN), Teheran (IKA) and
Tirana (TIA) must provide copies of travel documents of all passengers
on these flights in case they do not hold proper travel documents upon
arrival in the Netherlands and are inadmissible. Copies must include
the data page of the passport/travel document, the page with the visa
and the page with departure/clearance stamp, where applicable.
Non-compliance with these entry regulations will result in fines up to
EUR 11,250.- per passenger for the carrier.

You haven’t stated which country you were travelling to, but if it was the Netherlands then that is undoubtedly your answer. If it was a different country it’s likely that it was to cover a similar regulation for that country, or possibly just because the airline had been fined in the past for carrying passengers who did not have the correct documentation on arrival, so they were keeping a record on departure to be used to prove that the passenger did show the airline the correct documentation on departure.

A speculative answer.

It is becoming common for passengers to destroy or conceal their passports en route in order to try to claim asylum as an undocumented individual at the destination airport. That might be because they believe their claim will be stronger if they claim to be from a different country to their true host nation, or that while their true identity is established they will have time to begin legal proceedings in the destination country.

The airline involved will bear considerable logistical and potentially punitive expenses for transporting an undocumented individual. If the airline has photographs of the documentation for each at-risk passenger, the problem can be mitigated much sooner and the passenger identified with certainty and returned to the appropriate country.

See also Why would a visitor destroy their travel document?