My top 2 picks: 1) The fact that dialog windows almost always open on the wrong display if you have two displays and the external is the main one, 2) The fact that windows' positions/sizes are not remembered, There are a few other things (for example, occasional performance issues) but these two annoy me the most.

Aside from that, I absolutely LOVE Inkscape - there are no better tools if you want to have granular control over the SVG.

Edit: here's another one, not sure if macOS related tho - auto-selecting the parent when clicking the path underneath it. Because of that, I can't use a hotkey to switch the visibility of the selected path on/off (Inkscape switches the visibility of the parent layer instead, affecting everything that's inside).