Interesting floor decision at Bay 101 last night

[Tapin]

So I was playing 3/6 at Bay 101 last night, and the following situation came up.

One player bets all the way to the river, the only other person in the hand raises and calls the reraise. First player turns over J4o for two pair, second player turns over a red T8. Dealer calls the second hand as a flush (there were three diamonds on the board), first player says "I've got two pair", and the pot is pushed to the second player.

As the next hand is being dealt, a person who just showed up at the table and hasn't yet bought in says "Wait a minute, that wasn't a flush, he had ten of hearts, eight of diamonds. [The second player] only had a lower two pair." The dealer corrects her, "He had a flush."

The conversation continues throughout the next hand, and finally the floor is called with the turn just having been dealt. By now, the J4o hand is convinced he won the hand, and convinced he protested before the pot was pushed.

A five minute conversation ensues. No cards are played during this time. Finally, the floorman goes to talk to "his boss" to see if they're even allowed to check the cameras since the next hand has been dealt. Play continues.

Two hands later, floorman's boss comes out to talk to the table. Another five minute conversation ensues. Again, no cards during this time. They decide to review the tape, and confiscate the approximate size of the pot from the player who may or may not have had the flush while they're investgating.

About five minutes later, bossman comes back out and says, "First of all, where's the girl that started this?" He means the person who had just sat down; she had since moved to another table (again, before buying in at this table). He then explains that it appears that the second player might have had a flush, and regardless the first player wasn't protesting loud enough or fast enough, so the second player gets his money back. This of course takes another minute or two to resolve, and no cards are played during this time.

I was merely an observer to all this, who was getting mildly steamed about the number of hands we were(n't) playing while all this went down.

But my question is (raised at the time with the table, but not with the floor): How can they take $40 off the table? What would they have done if the second player had lost his entire stack before all of this nonsense occurred? And why "punish" the second player for the mistake of the dealer?

(The first player said he didn't speak up earlier because he didn't want to get the dealer in trouble; of course, this same dealer earlier in her down managed to forget to take the drop out of a pot that was checked down between two players until after she'd pushed the pot, and made the winner -- coincidentally, the first player from the above story -- pay it back out before the next hand was dealt... nice lady, not the best dealer I've seen)