When I was rendering last animation I found an issue.
I had instance objects with "Render instance" enabled.
When I was rendering a sequence, some or all of those instances where not rendered in some frames. It happened randomly.
What's more interesting is: when I stopped rendering. And started from the frame where those instances where not visible, they were now present. But after few frames they were dissapearing again.
Disabling "Render instance" helped. All frames where rendered perfectly.