Yes, Game 12 was quite crazy. It had gone on for 17 or 18 minutes before the clock-violation discussion. Yang had fouled 3 times (intentionally once) and Chang had missed 3 shots. And, critically as it turned out, Yang had used his clock extension.
After Chang missed the 5 ball (his 3rd miss), Yang began running out. He made the 5-ball and the 6-ball and immediately asked for the cb to be cleaned. The ref took all but 1 second of the 40-sec shot clock to lift, clean, and replace the cb. When Yang got down to shoot, Chang pointed out something to the ref, presumably that Yang had already used his extension. After an 8-minute discussion that seemed to involve quite a few people, Chang was awarded ball in hand and ran out.
So, apparently, the time the ref takes to clean the cb must be included in the shot-clock time (not an unusual rule). But, geesh, she didn't even get the cb off the table until about 28 seconds had passed, and essentially used the full 40 seconds.