I used to have this problem as well, but mostly with triples, where every single time I would get 1 or 2 100's. I think it's mainly due to a bad habit of spamming too fast that you developed unconsciously somehow. Strangely enough what helped me with this problem was streams. Because streams force you to tap to the beat and are also not stacked you need to flow with the rhythm and be more "in tune". After I started being able to do some short/slow streams I would just imagine that the triple is a really short stream and mostly got over the problem.
Also the reason why you don't have the problem with a circle on a slider is not that you're doing it better it's because slider starts are more lenient in timing.