What period are you choosing?
I think the three day option kicks the horse out on the third day, which really only gives it two days... you can see what day the boarding will finish on the horses page - you also have a button to extend the stay, although you then have to confirm that on the EC's box page.

Thank you for your suggestion of checking the period length. I chose 10 days though. ^^
"23/12/2025 The horse has been boarded for 10 days"
"25/12/2025 The horse has been boarded for 10 days"
"27/12/2025 The horse has been boarded for 10 days"
"27/12/2025 The horse has been boarded for 10 days"
(all for the same horse)
Yes, twice on the same day - before and after the update. I've had 54 boxes with <100% wear and tear for days now. The horse keeps getting kicked out.

I just boarded him again. This time I didn't just check the 99% boxes, but all the boxes. I couldn't find him, so I said "with boarded horse only" and a 100% wear and tear box is on the list.
That's him (click). As you may see, if you're checking this before the daily update, he appears to have a water trough. But if you check my EC, it says, I don't have any boxes with water trough, because it's one of the destroyed boxes.
It seems, he got moved into an already destroyed box. This actually explains everything:
* The horse gets kicked out with the daily EC update, because that's the time the game updates and checks the state of the boxes.
* The message, that a box has reached 100% wear and tear, appears, because this is sent whenever there's a box, which is at 100% wear and tear after the update, which contained a horse that got kicked with the update.

Apparently, I found a bug making it possible to move a horse into a destroyed box. (not intentionally though, since moving horses is random, as far as I know)
So I guess, the support actually is where I have to go. Sorry for the confusion, but maybe this has been interesting for someone else. Always learning something new. ^^