"This action was unexpected and unauthorized. Individual political protest contravenes not only company policy, but also our responsibility to create a more connected, caring, and civil society through shared artistic experiences. "
Emphasis is mine, but it seems it's because of it being about Palestine, because they had no issue with shows that specifically supported Ukraine.
The Opera's other location (Jubilee) had the national ballet of Ukraine, and they have the flag as part of the show
They also got some supportive articles written: https://calgaryherald.com/entertainment/theatre/art-is-healing-national-ballet-of-ukraine-performs-in-calgary-to-raise-awareness-funds-for-home-country
While I don't think the Calgary opera would find a Ukrainian flag be disruptive to a "connected, caring, and civil society" considering a good portion of the population is of Ukrainian descent; it's definitely tipping the scale towards hypocrisy.