Hi @Adam Love,
Thank you for reporting this issue. Would you be able to share a screen recording of the issue as it occurs? If it helps, there is a "Select" menu at the bottom of the right-click menu when you right-click in the Comp panel that will show all the layers that are under your mouse. If you use that sub-menu, are you able to select the Shape layers you need?
Thanks for any additional info you can provide,
- John, After Effects Engineering Team