However, I don't think users care that much about consistency, unfortunately (even though I think it's important aspect of design). Look at web, every website is different and it's considered a good thing by designers. There is no consistency on web and yet desktop apps struggle to compete.
With GIMP it's the sliders in the tool options. Once you have them figured out (the trick is, they behave differently when you drag on the top half of the slider or the bottom half ... it's indicated by the cursor changing, but still) they're kind of usable, but still awkward. If you don't know how they work (and they're quite unlike any other GUI widget I've encountered), you click and now your brush size is 1233.12 pixels, so you just decide to enter the value manually by keyboard. There's a couple of truly useless default values for some tools. Third, if you want to adjust or create a new brush, or gradient, the workflow has about 2 popup dialogs too many. I could go on ...
In InkScape, my main beef is the gradient editor. The old one was awkward and counter-intuitive when adding new stops. Then they made some huge upgrades (honestly, a lot of great improvements btw), also changed the gradient editor. Now it's slightly less awkward and slightly less counter-intuitive, but not much.
These are two great pieces of software and I love using them for the most part (although GIMP really needs to grow up and support 16 bit colour), it's just that these are some really odd choices for a couple of UI widgets that get a serious amount of use in most workflows. And I don't understand why, they could literally implement a design based on any vaguely similar control widget in other software and it would be 10x easier to use. Yet they choose to roll their own very unique behaviour that honestly just doesn't work very smoothly.
I' even doubt the premise that there are terrible open source UIs created by designers. The vast majority of OSS GUI apps were probably styled by programmers, and I think they proved quite well over last 20 years that they chose well when not becoming designers.
The problem with design is also that it doesn't work very well in the "bazaar" style of development. Consistency is possibly the single most important feature of good design, and it gets hard to achieve without central authorities.