It might be worthwhile looking more closely at the party losing equipment in the "known" stories. Usually it seems to be the Greys, and I suspect it is purposeful on occasion.
If you consider
operation Mincemeat, a true Alien intelligence could do very similar things with very Alien purposes.
Lets suppose the following, our Aliens are looking to acquire all analysis and research site locations. They are operating from an alternative time or dimension, and can only place systems and assets into our local space in a generic manner.
One way that would work is a shotgun approach, you crash a series of tracible objects that fall into the category of "shiny", and the pieces are distributed according to size to various important Human locations.
As an Alien, you now have the places of interest fully "triangulated", this allows you to use the advanced techniques inherent to your species and technological prowess to "do things".
Some of those things may involve tagging people who interact with objects, using the objects themselves as some form of interdimensional portal, etc.
Another stranger alternative is that a lost asset causes a glitch in time, which creates future conditions where the group sending the device does not send the device, and they don't know they need to retrieve it, because the timeline that would retrieve it has ceased to exist. Very weird stuff would happen under those conditions. I mean, you could end up with a Grey invasion force, which does the invading, but then finds their Masters don't exist to complete the takeover... quite what would happen there is entirely up for debate.