Hi Lukas, thanks for the bug report, we'll do what we can do to fix it.
We can't 100% align stuff with LaTeX though, just FYI, since Dynalist gives raw LaTeX for KaTeX to render, and we don't interfere the process. The LaTeX itself might be taller than the original line to look nice, resulting in slight misalignments.
The 3rd item in your screenshot should definitely be fixed. I mean that in the first item, it's also very slightly misaligned, which is unavoidable for now, sorry about that part.