Anyone else get the feeling...

that their ships are returning with far less than they should or that sometimes the ships that are sent out appear as though they weren't even sent out to begin with? I swear I sent out 3, but 2 of them didn't even go out and the 3rd one had FAAAAAAR less loot than it should have. Game is full of bugs.. who knows what's going on.

Was it because the "favored resources" quota was met and it switched over mid mission and therefore cancelled two of the ship?

Less loot is conspiracy talk. I've done thousands of ships at this point with varying sizes including some of the 50m ones and the only significant change in loot was with the shipment rework several weeks ago.

The vanishing ships is a bug that has been happening all league. Lost a few 100k ships that I didn't understand why at first, but mostly lost 2 bar ships once I confirmed it.

Favored resources from quota being met has only added a random unique to the table plus a refresh for boosted resources.