OK, as a hint for others: I found out, that some tables had different database collations. Thats why some migrations didn't work. Its most likely due to the fact, we imported an existing Matomo instance into cloudron: https://forum.cloudron.io/topic/10759/migrating-matomo/2?_=1762191084826
With help of AI we fixed thos database errors pretty quick now.
Annotations work again. Also another plugin in Matomo, which complained about missing tables.