The bug is that resources from scrapped facilities, despite showing up immediately when you're playing the turn, vanish without a trace in turn processing.
Resources from scrapped ships come in when the ship is scrapped, which happens when it executes its orders for the turn. When that happens relative to any retrofit orders depends on the speeds of the ships involved and on their ship ID's. Resources from a ship with speed 5 will never be available on the same turn to retrofit a ship with speed 6. If they both move on the same day (eg, same speed or speed 10-13), it depends on ship ID, which I most recently explained in
this thread
Note that bases and ships with no engines "move" on day 0, so resources from scrapped bases will always be available to spend on retrofitting mobile ships, while scrapping mobile ships can never pay for retrofitting bases.
Also, there actually is one way to get resources from scrapped facilities in simultaneous play - abandon the planet and answer the prompt about scrapping the facilities with "yes". When the abandon/scrap order is executed (on day 0), you will get the correct amount of resources for scrapping every facility on the colony. Of course, this does completely destroy the colony, so you probably don't want to do it very often.