Unfortunately this is one of the more idiotic design decisions with the game, assuming it is by design.
I'd raise it as a bug report, but i suspect i'd get the dreaded "working as intended" reply. I'd rather try and live in false hope that its just a bug that FD one day sort it out.
To work around it, when you stop for the day mining, go hand in your cargo then go out again with just limpets in your hold.
It would be nice if there were a persistent flag to allow a session to be re-established with the same number of NPCs there were when you logged out, wouldn't it? Spawning an instance appears to take no account of the state when you logged out. Has the bug been fixed whereby pirates demanded that you drop your tasty limpets because they mistook them for cargo?