IMHO, you should select your favorite travel sites, and add in the actual airline's site and check ALL of them every time! I have long since given up trying to figure out why fares come and go. I think I need many more lessons on chicken entrail reading before I enter the hidden innner circle!

FWIW for example, I have more often than not found flights intra-Europe on BA metal that price our WAY cheaper on AA.COM than on BA.COM or Expedia, and so I include AA.COM as one of my research tools. Once in a while I find a domestic fare on AA that does not even show on ITA! Other times, I find a fare (more accurately a routing) on Expedia I just can't duplicate on AA.

Bottom line: I can't figure it out, so go figure!