corps have a spending limit, like countries and enterprises. if you have the space parts, and manually sell them to your shuttle corp, you'll run out of spending space when you get to extensions, or fuselage, if you go strait down the list. and when you don't have enough spending space for parts, you'll get that message, even though its not an actual shuttle.
the thing to do, if you have the parts, is to increase each of the shuttle parts to like 20 game months, then go back and max them out.
and very, Very important. after you supply your shuttle corp, manually put money into it. I max out the available cash in my shuttle corps, every time i resupply. about once a week.
you only would ever notice the corp spending limit, with shuttle corps, its like 400B or such for maxed out space parts, their aren't many corps that have that much value in their raw material. and i'm not 100%, but i do believe the GM have increased the spending limit, and max cash for shuttle corps, for this very reason.
In the past, it would take a couple of weeks for shuttle corps to fully supply, with the lower limits. and when we could buy space parts off the world markets, (they used to be like any product,) they would often buy so much, that they'd close before they ever produced a shuttle. we used to have to max out the cash in them, like once or twice a day, for a couple weeks, or you'd have to start all over. the GM have improved that, so that they aren't so hard to keep going.