Basically the only time this happens, at least for me, is when I am upgrading from shuttle to assault shuttle or adding in pinances then I end up with a temporary number of excess older smallcraft. They get moved by the CFN to places that need them. I would personally not worry about it unless you are talking about armed smallcraft of some sort or someone is clearly using them for colonization purposes. Otherwise they should be absorbed by the players other units inside of 5-10 turns.
Again if someone is abusing this then you can charge them maintenance on the shuttles and back date it and put it in the misc cost area of the turn balance window. I would charge them in this case the cost of a spaceport's maintenance fee for a PDC on highest population centre in the system. Basically if they are using up space in the free civillian space port they pay.
I should also point out most of the time these systems, in my case, I have a PDC with a spaceport that can support the smallcraft so it isn't an issue for me (I'm paying maintenance on the spaceport and its capacity can support the shuttles). For my NPC partners which had this issue I'm not sure this is always the case but they have a lot of bases and such that could be considered providing support for the excess smallcraft. I'm not sure where the heck the shuttles ended up when I converted over to assault shuttles actually...their homesystem I think.
If the players are abusing the system it is worth doing something about it, otherwise it isn't I would think worth the hassel of bothering about. A few gentle reminders should prompt the player to do something about the stray smallcraft... As SM you can always delete them if they don't catch the subtle, gentle hint.