This is often overlooked and it's a fair point in defence of the people working for Yandex. You can't judge someone just for working for Yandex or even most Russian companies. The people who have voiced concern are already out of the company and it's perfectly reasonable that the rest would like to keep their jobs, especially in uncertain economic times with all these sanctions against Russia.
However, this also implies that Yandex, as a company, cannot be trusted. It's not the researcher's fault, but they simply aren't allowed to work in a way that doesn't reinforced the Russian government's bias. As usual, the Russian government is the real villain here, but its authoritarian rule "infects" any company and country it has control over.
It can be assumed that the people working for Yandex are also victims of their abusive government, but that doesn't change the fact that their work is unlikely to be trusted outside the Russian sphere of influence.
From what I've seen, telling the truth in authoritian countries doesn't end up well.
To the best of my knowledge, they are a Russian company - it's not like they can just tell the truth and move away from Russia that easily, so I think (and hope?) they're just playing a political game.
They will simply have their company taken away from them.
Nevertheless, they had many years before the war to start marking their news as 'Official'. Or sell the news service. They certainly could have done so. This would have solved their image problems.