At least twice that I've played, I've gained the Inn from the trash and the box that allows you to select actions to shuffle back into your deck is bugged. Multiple actions get stacked, and when you click on them, it allows you to click that stack once, which applies an X over the stack, but you can't interact with that stack anymore afterwards. In other boxes like this, a number will appear to let you know how many you're selecting, but it doesn't do it here.
I can't remember how I gained the Inn in the first game. In the last game I just played, I used a Rogue.
That is unfortunately a rather long-standing bug that happens whenever the Inn is gained from the trash, as you noticed.