Not sure if this is relevant here, but one source of confusion can be that the TaskPaper format is a purely tab-indented outline.
In the following example, Beta, Gamma and Delta are not children of Alpha (they are peers), and will not be collapsed under it:
Alpha:
- Beta
- Gamma
- Delta
(only tab-indented items are children of preceding project lines. If the project is itself indented, only items that are more indented descend from it)
See the example at: