You put ONE GEM inside of a dead kobold, and for the next TWO YEARS your players butcher the guts of every creature they come across.
How to turn this into an example of agency instead of an automatic action?
- Have a consequence for taking this action
- Provide clues in the environment or the encounter that the creature might have eaten something
Much of what a relevant consequence is has to do with what type of game your are playing. In a megadungeon, having the butchering take a turn and grant a +1 to the next one or two wandering monster checks is a reasonable and significant penalty.
In quest based small site adventures it becomes more difficult to institute a reasonable penalty. Perhaps a penalty to monster reaction, or in the likely event that reaction rolls are not used in your quest-based game, a penalty to social checks or even charisma for a short period after butchering the creature. Certainly in a more social game, providing a -4 penalty to diplomacy, gather information, and bluff checks (along with a +2 bonus to intimidate checks) is a reasonable penalty (or a -2 on reaction rolls).
What can clue you in that a person or animal might have something hidden inside their stomachs?
- A wild animal lair with fresh kills of humanoids
- A corpse nearby something subtly missing
- A prisoner being interrogated
- Nearby non-food substances having bite or teeth marks
- Interesting items found in stools or obvious elimination areas
These need not be obvious. A fresh kill in a monster lair can be described as having equipment, but with his guts and groin chewed out and eaten. Searching the stomach of the monster will turn up a belt buckle and pouch. The same with leaving a fresh kill that is missing a hand, where you find a ring inside the target.
The subtle missing item can be something very obvious i.e. "There is a circle of dust where something once stood on the table" or it can be more subtle "You find paper and pens inside a drawer" where the stomach contains magical inks. The corpse doesn't necessarily have to be in the room -- the players can kill it nearby and be forced to connect the missing item with the monster that could have eaten it.
The other two are obvious clues that if downplayed only active and experienced adventures will follow up after itemizing the treasure they found.