Because there is liquid inside of it.
I was once traveling with someone who had cans of tuna in his handbag and was fully prepared to open it up on the spot, drain the water, and put the tuna straight up in his pocket, but thankfully we were able to send another checked
That reminds me I once by mistake left my toothpaste in my carry-on, when they discovered it, they pointed to the size printed on the tube and showed how it's over the limit. it was half empty I told them! To no avail..
TSA = Toiletry Search Agency
ETA: The life hack:
Print a replacement 1ml water bottle label, and enjoy a safe passage! (YMMV)