For me it's the colouring process, sometimes the inking. Worst of all when there's backgrounds to do because I'm very weak at them 8(
I'm surprised nobody's mentioned this yet because it's such a pain for me but speech bubbles. I alwats mis-calculate how much space I'll need on at least one panel.
When I was deciding the art style for the comic I purposefully decided to make the backgrounds lineart looser, sketchier, so I wouldn't lose my mind over them 
It's a life saver! On the other hand though, scenes with many many characters in them get really tedious for me... It takes forever and at least one in the bunch ends up looking like a moron, usually!
For me it's the part where you pour your heart and soul, all your spare hours, and decades of painfully acquired talent into something for a few hearts and some comments, then you log onto Facebook to see a looping video of hamsters jumping between rugs with one and a half million views.
For me it's the character gesture and expression, it's hard to make them look right and natural..
For background you guys can try Google SketchUp, I see a lot of webtoons use 3d to make their background.
STORYBOARDING. easily. Planning out appealing compositions and making everything seem appealing is tough
Thumbnailing is a headache if I don't have a clear vision of how certain events progress. When I have a clear idea? Get through 10 thumbnails worth of pages. When I don't? it takes me literal weeks to try to figure something out. Then trying not to repeat the same layout. Not repeat the same angle. make sure it makes sense........
Currently for me, it's the whole layouts/sketching/lineart phase. I LOVE inking; I dont even have an issue with coloring- but the drawing phase of making a page has been really killing me short of lately. I've been dragging it out until I get to the point where I say "f**k it" and just do the page; afterwards, the cycle starts all over again...
THIS..!
For me when I making Sang Kong1, due of color blindness the most tedious part for me are coloring or to be exact picking color, I must use ref and eyedrop tool to "steal" some colors.
second part, probably more personal problem when my family see me drawing comic, when I stop and rest they ask why I don't draw and act supportive, when I draw they talk to my back (literally) most of them mockery, when I talk back they use words like "it means we concerns about you". I choose not to listen to them anymore except if it was important, but still.. it's annoying.
Sorry about my English, it's not my native language
For me, it's thumbnailing, or paneling. Deciding which size one panel should be or which form it should have, particulary.
I've always had the hardest time with backgrounds. There are some instances where it's a little less challenging but I tend to avoid then just so I don't have to stress about it.
I use to have a big issue when it came to colors but I think with time and practice it's gotten a little easier. What's harder is making sure that characters are staying on palette and then working on color temps for the setting.
Beyond that I can agree with the challenges that come with paneling and speech bubbles. Spacing things out properly between fonts and avoiding tangents and other things can be really tedious so it's probably my biggest issue 
Drawing little tiny people, like in wide background or distant shots.
Their faces/heads always end up disproportionate to the rest of their bodies and I have to use the transform tool a billion times.
I actually quite like those guys. Although, yeah, I do admit it can induce some anxiety trying to make them different. Isn't there a quote by Renoir or someone like that about how you can only draw so many leaves before you start drawing the same ones over and over?
Maybe it would make a funny story to have a comic where all the characters are made up of those guys, with their busted body proportions and sometimes yes, sometimes no faces.
Certain backgrounds, and making last minute corrections are consistently the most tedious parts for me. There have been many pages where I didn't catch inconsistencies between panels until the last step of the process. It's so annoying because I was just about to finish the page and add it to my buffer, but I'd rather correct those errors at the last minute than to not notice them for days after uploading the page!
I use vector graphics, which makes architecture easier for me to draw, and keep consistent compared to when I draw them freehand, but nature backgrounds are much more difficult and tedious to draw with vectors.
Thumbnailing page layouts is sometimes easy for me, but only if I have a very clear idea in my head for how I want a page to turn out. At other times I don't have such a clear idea, and then it's tedious using trial and error to figure out the angles, what type of shot I want to use for each panel, and how many panels to put on the page.
Coloring by far. My tablet PC is also over 5 years old, so waiting for it to freeze or recognize my pen input is also a big problem. When those two things happen at the same time? CHAOS.
