If your dropship returns with more loot than can fit into storage, items will be auto-sold to make it fit. But the user has no control over the process. At one point I returned from a mission and was immediately going on another one and found that all my medkits and plasma blades had disappeared, along with other useful items. Medkits are easy to re-buy (if you notice they're missing), but other things are more rare. Plus you always lose money when selling-rebuying on the market.

My suggestion would be to pop up a sell dialog to force the user to sell some inventory and not let them proceed until the retained inventory will fit in storage. Same thing that's done automagically now, but give the user control over it.