This might be hard to diagnose without seeing your data or understanding how things are tagged.... the "rates" aside, what do the raw numbers look like in your funnel? Are there ways for people to bypass clicks during the flow (which would result in more Page data, than Click data.. and this could significantly change the calculations). Is your funnel based on Visit or Visitor? Is it looking at Eventual Path or Next Hit?
As with anything, my first recommendation is to test the flow(s)... try acting like a user... don't just follow the path you expect the users to take, try to take unexpected paths... try using your browsers back and forward buttons (this will then track additional pages but not your custom clicks), try going straight into pages bypassing some of the steps, etc. Can a user leave the site open for a hour, then come back and resume a journey?
Watch the data that is sent to Adobe and really try to understand the nuances between different behaviours, and what that does to your data collection.