This is not that unusual. It happens to me every time I forget to hand over my Dutch residence permit with my (non-EU) passport when leaving the Schengen zone from Schiphol. The border guards are absolutely meticulous about flipping through the passport looking at the entry and exit dates in the hopes of catching a potential overstayer. They're almost always super disappointed when I realize what's happening and hand over the card.
The threat isn't "we're going to keep you here because you weren't allowed to be here," it's "we see you have overstayed your visa and now we're going to make sure you catch your flight out and ban you from ever coming back."
The threat isn't "we're going to keep you here because you weren't allowed to be here," it's "we see you have overstayed your visa and now we're going to make sure you catch your flight out and ban you from ever coming back."