When you add a Southpole contraption and click on the LFO1 and LFO2 tabs, the controls are not aligned the same (the LFO2 Period and Phase controls are narrower). Weird thing is, when you switch theme from Dark to Light or vice versa, the alignment fixes itself.
Also, two other GUI inconsistencies (although both extremely small and unimportant):
1. Some windows (the Time Signature selector, for example) have the "close window" X button in the upper right corner, although it's not active, could that be removed? I always try to click on that first when cancelling instead on "Cancel" :)
2. When moving the dividing line between the Snapshots list and Parameter list parts of the Metasurface widow, at one point the dividing line "breaks" and shifts one pixel in the area near the New Snapshot button (this is probably not even worth mentioning, but whatever :-)