For example, problems like this one. Or the confusing 3D navigation (switch to Gesture or TinkerCAD mode in the Settings), or the non-interactive view cube. And many other gotchas and paper cuts that can almost all be changed with a few clicks to make it more intuitive, or just more similar to popular competition (e.g. the OpenTheme add-on gets you that Fusion look you see in many FreeCAD tutorial videos).
It's a classic pattern with long-running FOSS projects. The authors get somewhat blinded to the pain because they're used to it, plus change is difficult for the established userbase. There's also a feeling that emulating competitors is surrendering one's own identity, and the idea that some of the rough edges are justified by "the powerfulness". Thus radically changing defaults, streamlining, simplifying and even just matching user expectations is often perceived as "taking the power away" and really difficult to have the daring-do to just do. Even though on the other side of the transition a much larger and happier userbase awaits.
A lot of FOSS projects eventually do mature to the point where they can pull this off, and I think there's real signs that FreeCAD is starting to get there. The upcoming 1.1 release has a ton of modern UI catch-up, such as on-canvas gizmos, and a few good defaults changes.
There's a lot more work to do, but like others I have the feeling that FreeCAD may well be approaching its Blender/KiCAD moment. I suspect becoming a contributor right now could be good fun.
I speak from experience! We've to some extent been on a similar journey with the Plasma desktop.