A bit late to this topic I gather, but highly agree with this. It is immensely frustrating to deal with these problems, especially as a paid user, expecting complex conditional smart animations to work flawlessly. Not to mention how frustrating it is to present projects to clients.

This problem feels entirely like a case put on a lower shelve by the team Figma unfortunately - even though it’s tied to most of the paid functions -, I wish it would get prioritised over some of the needless changes that get reversed anyway recently.

One can only hope.

If you set the main frame containing the sections to a fixed width, such as 1440 x 1024, and enable scrolling within it, you won’t face this issue. However, if you set the main frame to "Hug" height, then naturally, when components like an accordion expand, the height of the main frame will also change. This causes the entire frame to readjust, which results in the content jumping back to the top.

To avoid this, it's recommended to use a fixed height with scrolling enabled rather than a dynamic height that adjusts with content expansion.

I think I’ve figured it out. Well for me anyway.

On the parent frame/screen where the animated elements live set that parent frame to vertical scrolling within the prototype options.

I now have multiple animated expanding (up/down) sections within one screen and it works with smart animate.

Hope this helps.