people are often hard to understand. a big cause is the use references like "those", "this", "that", "the argument above", "in your example", "thing", "stuff", or "it". it's better to use less generic phrases like "the argument about cats" or "the example about pizza" or "those stones" or "that criticism of sharia".
if there is one confusion about a reference (or anything else), be extra clear after that. don't keep using other references and shortcuts to try to fix the first one. don't risk stacking up misunderstandings. that gets into a huge mess real fast.
when things are going wrong, switch straight into extra safe mode. one problem is a sign there could be a bunch more in the area. don't wait until you see five problems before you start adjusting.
writing out what you mean in longer, fuller sentences is not that big a burden. it's way better than having a bunch of misunderstandings. it's ok to start with some shortcuts initially (although people overdo this), but if it goes wrong then take a break and be as clear as you can.
when in doubt, maximize clarity.
You can improve clarity by writing short and simple explanations. A bit of repetition is OK, too.
Keep it one topic per paragraph, make point at a time. Don't get all ambitious, overreach, and say 20 things at once.
It's ok to be somewhat "pedantic". A pedant is "a person who annoys other people by correcting small errors and giving too much attention to minor details". Correcting small errors helps avoid misunderstandings! Getting the details right improves clarity.
Being kinda pedantic is especially valuable when there's miscommunication or misunderstandings going on. Then you should focus on slowing down, correcting errors, and not letting a bunch of little detail misunderstandings build up into a big problem.
If you have small misunderstandings, you should try to halt the misunderstandings there. If you instead pile on more small misunderstandings, it'll grow into some big misunderstandings.
If you can be aware of when a discussion isn't going great, then you can adjust. You should be happily willing to use your highest levels of clarity and patience whenever you see a few signs it might help.
And most people have frequent misunderstandings in their discussions already. Until those are better managed, you should just maximize clarity and patience at all times. Practice it, get better at it, see how the results are different.
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Acknowledgments: some ideas presented are modified from, or inspired by, ideas from Karl Popper, Ayn Rand, David Deutsch and William Godwin. Thank you!