Yeah, I have exactly the same problem as you, which is why I had to change my style to thicker lines that close all the way. when I was doing a style with open lines, I used a lot of screentones to shade, which allowed things to be imperfect without it being a problem, and I could get shading down fairly quickly, which was perfect for black and white (which is probably why manga's used screentones for eons), but doesn't work for color.
Also, I find that the paint bucket in CSP tends to leave gaps, which don't always close where I want them when I use the gap fill tool. So I switched to using https://www.flatto.nl/ (it's a free browser site that will do a flats for you so it defines selection areas, that you can select with your wand without aliasing on, and then you can fill in a separate layer) and after I use flatto.nl I will go in and refine those areas with a brush set to dissolve since it still won't catch everything. Thing is flatton is really sensitive to gaps more so than CSP so it might not work, but making a flatting layer has helped me a lot with just defining where selections are going to be so I stop getting these surprises.