Yes, nested nodes can cause problems.
Nested nodes are acquired when you work on an object when it is part of a group or shape, and then ungroup it.
Transformations and texture applications that were applied to the group are retained in the nested node. Strata is usually pretty good at clearing transformation-only nested nodes, but a nested node has to be retained to retain the texture application.
It's better to not apply textures to shapes or groups and then ungroup them. Transformation nodes alone should clear okay when you ungroup, but texture applications will require the nested node.
There is a thread on the StrataCafe that discusses nested nodes: