The most common mistake is working on the live site. A course site has students inside it every day, and a styling change that hides a button or breaks a quiz page is felt at once. Work on staging, run through the whole student path, and only then repeat the change live, outside your busiest hours.
The second mistake is stacking fixes. If a screen looks wrong, resist adding a custom CSS rule on top before you know why. Check whether an old rule from a previous theme is causing it, or whether a LearnDash setting is changing the template. Remove old rules first and add new ones last. Keep a short note of every custom rule you add and the screen it fixes, so whoever maintains the site in a year can tell what each rule is for.
The third is adding the community without telling students. If BuddyNext spaces appear overnight with nothing said, students will not find them. Send one email that explains where to ask questions now, pin a welcome post in each course space, and add a link to the space from the course page. The community only works if people know it is there.