I’ve been scratching my head about a potential solution for this for a while now:
Whenever entities that have special opacity are behind another entity with special opacity (i.e. a cutout tree behind glass) it causes the entities to appear/disappear based on what angle you look at it from.
This is likely be related to the order of rendering of transparent meshes that is explained here:
How to work around it would depend on your specific app and logic. Putting them on different render layers so you can ensure that one set of meshes is always rendered before the others. Splitting up models if this is a large mesh instance of multiple trees etc.