Can you then provide an example of this document ?
What I am trying to explain is that when printing, special CSS rules will apply. The link I shared is to help debug and find the rules that is not applying to print mode, and why.
Once identified we can then know what to do. It could be a user's CSS rule, a Bootstrap's Rulle, a R Mardown internal CSS rule, a Pandoc's CSS rule...
You see that this is several place this could be. I need more element to solve.
I don't know if you search around, so you may already have seen that, but here is a related problem because of Bootstrap own rules
Using bootstrap v4 solves it. Maybe this what you encounter.
Hope it helps