On the federal level, the filibuster is an obvious example of a an anti majoritarian rule that creates perverse incentives.
Going deeper, the way that the individual houses are structured gives significant power to committee chairs who gain power through seniority and fundraising for their parties, which creates centralized points of leverage for lobbyists.
What we’ve seen over time is that fewer and fewer bills get passed, and individual bills themselves get larger. This is a result of rules and customs changing within the house and senate themselves that have made it harder and harder to pass small bills, so everything gets rolled into monster packages and the process get more obscured to people who are on the outside.
The thing is that all of these rules get set by majority vote. Leadership elections happen by majority vote. Changing rules can happen without consent of the other house. The issue is that there’s very little understanding or focus on why they are important.