Hi, I've been having the same problem!
I have a Notebook open in ArcGIS Pro (v3.1.2, Win10) and whenever I click into another Pane (Attribute Table, Catalog, Geoprocessing, etc.) and then back into the Notebook, the Notebook suddenly jumps/rolls up a bunch of cells, causing me to lose focus every time I click outside the Notebook. If I have the Notebook Pane opened on the second monitor (and the rest of ArcGIS Pro on the first monitor), the jumping/scrolling also happens when I switch to another program window and then back to the ArcGIS Pro Notebook.
This is very frustrating, makes very hard to work with Notebooks!
Note: I noticed that the problem is not happening on my colleague's computer, who has ArcGIS Pro v3.0.4.