Frustrating UI design
Many of the important open-source programs suffer from terrible UI design, which make it difficult to learn, understand and get things done. I believe this stems from the fact that the developers are also designing the UI, whilst being unable to relate how new or novice users would use the program. I also believe they take shortcuts to get things working quickly without being concerned how this works out for the workflow.
Blender has the exact same problem. I've been using it for many years now yet even the newest version is frustratingly difficult to use. I've learned to cope with it, but the overwhelming number of sliders, buttons and checkboxes (many of which I'm completely in the dark what effect they have) and the illogical tab structure make it a struggle to get things done.
I always feel that commercial programs are easier to use because there's a dedicated UI design team that observe and record how users use the program. The KDE team has learned from its mistakes and now has a dedicated UI design team that oversees all KDE development.