Vertical base and interval elements stored outside of complex

To be more clear than the title, I have multiple vertical alignments under one horizontal. The problem is that I also have a large number of isolated elements with with interval relationships to each other (i.e. they are top level elements, not stored under the umbrella of a complex element). But if I try to delete these elements or remove rules, I find that it deletes sections of my alignments.

Why has this happened and how can I get rid of these additional elements? It wasn't bothering me too much before, but now I'm finding that I can't create a copy of the alignment and this is the only thing that's unique about it compared to others that I am able to copy.

Thank you

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