Hi Aurelie Shapiro,
I took a look at the workflow and initially saw the same thing when rendering a line in the 3D Visualization theme. After some further digging, it looks like reason for the extruded cylinder is that the app picks the first layer in the scene's Table of Contents for visualization, and the default visualization mode is point extrusion.
To get around this I added an empty Feature Layer above my line Feature Layer in the scene's Table of Contents. After making this change, my app rendered the line as expected:
Hope that helps,
Peter