1) The Liberty's move also dramatically affected revenue. They went from about 10,000 tickets sold per game on average in 2017 to about 2,500. You can't find figures for average paid ticket price, but from the list of the price of different tickets, $25-$30 seems like a reasonable guess. In which case, somewhere between a quarter and a third of the league's losses are the result of this move. And it wasn't just the Liberty; the Washington Mystics also moved to an arena that has a smaller capacity than their 2017 average attendance.
2) The NBA's original rationale for creating the WNBA wasn't to make money directly. It was to use the league as marketing for the NBA itself. The thought was that having a women's league would increase interest in the sport of basketball and thus create NBA fans, especially among women and girls. We have no idea how successful the WNBA has been at doing this. I'm pretty certain that the number is greater than $0, but you could cite a very wide range of numbers that I would find plausible. So, the real net loss for the league is almost certainly lower than $12 million.
Note that this does not constitute a subsidy to the WNBA or some sort of cause. Whatever the marketing value of the WNBA to the NBA is, that's money that the WNBA is generating for its parent league. It's just money that does not show up in the WNBA's P/L statements.
3) The WNBA players are clearly at least somewhat skeptical about that $12 million figure. One of the primary reasons that they voted to reopen the CBA after this season is that they want to examine the league's books rather than just relying upon what the NBA tells them. It's possible that this is related to point #1, and they want to see how much of the damage to the league's finances was self-inflicted (or Dolan-inflicted, if you choose to view him as separate from the league). It's possible that it's related to point #2, and they want to see the NBA's estimates for how valuable the WNBA is as a marketing tool.
But there are dozens of ways to cook the books of sports teams and leagues. There are even more ways to cook the books of a league that is effectively the subsidiary of another league. Do WNBA teams pay market rents to use NBA facilities? Is the WNBA's revenue from TV deals entirely independent from the NBA's own deals? We don't know the answers to these and many other questions, and neither does the WNBPA. Regardless, until the NBA allows independent examination of the accounting, we don't have any reason to accept their claims as necessarily accurate.