hard to say! i do think the most likely thing is that the packages were with a character who wasn't selected? the game tries to only show markers for packages that are contextually relevant, so if you have a pilot selected it will only show their packages -- but sometimes its not as helpful as its trying to be. also speaking for myself i have definitely accidentally handed the package to the wrong pilot quite a lot, and then got to the destination and be like "oh crap, you legit don't have anything for here" :D
i have seen at least one streamer hit a bug tho so who knows. the packages are not supposed to expire and still give you $10 even if you hand them in late
after the jam is over i intend to do a lil ux pass if i can and try make the game a bit more approachable.