It's more of a married segment availability issue. Google flights shows those 4+ hour connection with a lower price than on AA.com.
e.g. SAN-LAX-YVR
If you break it into two segments:
SAN-LAX ...N9
LAX-YVR ...N9 (after 4+ hour connection)
But if you do it as one segment:
SAN-LAX-YVR ...V9 N0 etc.
Since Google flights mostly use married segment availability for up to 4 hours connection (which is the norm for most US/Canada flights), AA allows connection up to 18 hours to/from Canada. Hence it will error out if you have a 4'01" connection because Google assume both segments are available in N but it's not when you click onto Google (you can't go around this and use OTA as well).
IME, if you force an overnight connection AND if your connection is between 12-18 hours, it will give you the 2 segment availability that you want otherwise it'll revert back to the married segment.
Hope this helps!
PS: Same goes for QR flights as well but you can't do anything except rely on married segment for anything less than 24 hours. You could have a 23'59" connection at DOH but it'll still be married segment.