I have MacBook Pro (MacOS 11.2.3) running Logos 9.4b3.
This is a long-standing bug, but I just realized what causes it.
I like to set program scaling to 80%, but it appears that this causes the length of the Table of Contents panel to be calculated wrong, and I often can't scroll to the bottom of the TOC.
Here's an example with the TOC scrollbar at the bottom, but the TOC is not at the bottom:

This happens in any resource, not just Bible ones.