It could be for many reasons.

Sometimes a travel portal might be showing a fare that's no longer available, and you only get notified of the correct fare when you click all the way through and attempt to make a booking (I've had that happen to me many times on Expedia in pre-covid times when I used to book with them).

Also, it could be that the different portals are in fact showing different fare classes - sometimes a site may show basic economy fares as default, while other sites default to standard economy. Are you sure you're doing a like comparison?

If a flight is particularly inexpensive, it might be that the portal for whatever reason is offering a discounted consolidator fare - although that tends to occur more with package deals than with flight-only bookings..

And sometimes things are just weird. I've been able to get an Expedia ticket for less than the exact same flights booked directly from the airline, for example - no idea how or why, but I didn't complain.