You mention that it is a company paid stay so, if the company paid the hotel directly, you are very lucky you got points to begin with. Honestly, I think you're overreacting for 1K points when you got a couple thousand, most likely, that you weren't even due. If you changed your preference after check-in, it's understandable that the 1K points did not post.

Frankly, you got everything you wanted...and more...so I'm uncertain what the beef is.

Bobette