Skyscanner

Are you comparing apples to apples? Same flights, same airlines? You don't book the flight with Skyscanner. You select the flight you are interested in and it pulls up a list of agencies to book it with- the airline (perhaps one you've never heard of) as well as 3rd party booking agencies.

Have you also checked your options on Google Flights?

Skyscanner is basically just for searching all options so you can see what is available.
Then you will book flights directly with an airline of your choice.
Don’t book with third party agencies such as Expedia, CheapoAir, etc. no matter how good prices look there.
If you have any problems with your flights, booking direct with the airline is a better way to solve them should they arise.
If you’re looking at Skyscanner, be sure you are looking at prices in Canadian dollars.
Prices there won’t reflect cabin choices, seat preferences, baggage fees, etc. which is why the difference.

Skyscanner lists the agencies that will process your airline ticket purchase. There usually are several of them and they are assigned a numerical rating between one and five that is based on customer satisfaction with that specific agency.

There are some such as Orbitz and Smartfares and one called StudentUniverse that I would not use because their customer satisfaction ratings are in the basement. But it would be wildly unfair to broad brush all of these agencies as being unsatisfactory or unreliable.

Would you avoid reserving accommodations through Booking.com rather than always reserving directly with a hotel or other property? Not likely.

In fact, Booking.com now is one of the agencies selling airline tickets. So, if someone uses Booking.com to reserve accommodations why would they then avoid using Booking.com to reserve airline tickets?

I have booked flights many times through Trip.com and JustFly.com as they have high ratings approaching a perfect “5.” I have never had a problem. In the event there is a problem, there is a customer service division that’s available to resolve issues. So, I do not agree that you should always book directly with the airline which, in some cases, actually may have a lower rating than some of these ticket agencies. When hundreds of dollars can be saved, it’s irrational to rule out saving money in each and every case.

Based on my personal experiences, when stranded at airports in Europe because of regional flights gone awry, I walk to the service counter of the branded carrier and resolve the matter....in person. This applies to codeshare and other flights. Assuming like like, I'd rather not make a long distance call to a third party, somewhere in the world and seek a solution to an immediate problem.