One thing that has caught me off-guard multiple times, sometimes in a really bad way, is the auto-replacement mechanic throwing away an inventory item when i only wanted to swap the part on the ground with an equipped part.
For example, when autoreplacing a Storage Unit, Storage Units with less capacity can be thrown away.
If i have a damaged Large Storage Unit equipped and a Medium Storage Unit in inventory, Auto-equipping a new Large Storage Unit from the ground equips the new Large Storage, places the old Large Storage in inventory, and drops the Medium Storage.
However, in most situations, when i have a Storage Units of lesser capacity, than the one i currently have equipped, it's because i need a backup in case i can no longer support the bigger one (for example, if my only weight-supporting utility gets destroyed) or if i plan on switching to a Storage Unit of lower capacity (transitioning to flight, losing mass to go full combat, and so on).
So, picture me, with a damaged Large Storage Unit, and finding a newer one on the ground. I swap it out with my current Large Storage Unit, effectively "repairing" it. However, i didn't notice that it made me drop the lower-capacity Storage Unit i had in my inventory, which i was safekeeping for later, only to replace it with the now useless damaged Large Storage Unit.
*Later* Now to equip my... Where's my Medium Storage Unit?
This has also happened to me with other parts as well, including weapons (for example, an Enh. Force Rifle i wanted to keep for the positive salvage and high critical chance). Sometimes i notice it, other times not so much.
My suggestion is an option to prevent Part Auto-Replacement from replacing both an equipped item and an inventory item. Or at the very least, add something that warns/notifies the player that an item from their inventory was swapped out.