You could do bigger hitboxes, and in the case where multiple overlap where the player clicked you assume they wanted the one closest to the mouse.
I love this! suddenly making me feel/realize I over-thought things!
Great Idea and I'll be sure to add it. (once the Jam is over)
One slight detail though, is it that the dots themselves are too small, or that you need to be too close to the dot to register?
One unfortunate thing that happened with the game is screen resolution affects the game resolution. Higher resolution screen may get smaller dots and that might feel harder too (it has its own pros too).
I personally didn't have a huge issue with the hitboxes, more just spitballing ideas. Though in general I agree that hitboxes for good things should be larger than the model (easier to collide with, select, pick up, etc), and hitboxes for bad things should be smaller (more forgiving when the player just barely grazes a hazard, etc)