Putting a unit on the sacred site didn’t stop the timer.
You can see that the unit is on the site and the UI in the top left shows that the sacred site started decapping.
But the timer still went down.
twitch clip clearly showing the bug
It was a custom game during the qualifiers for the Elite Classic 2.
Map was Dry Arabia
Players were 3D!CAT vs VanDerDorf
Civs were Delhi and Malians
If you need any more information please let me know.