First, home inspectors are paid to find problems. So even in the best of houses, there will be a long list of items--mostly inconsequential. (And I understand that--the buyer's paid $400 or so for an inspection and wants more than something saying the house is in good condition.) Those long lists of trivial items can scare off buyers. Now, if there are any serious problems or concerns, by all means put them down. That's your job. But sometimes it seems as if an inspector is searching around for something, anything, to list just to prove he's done his job.
Second, I've found that a lot of home inspectors come from one particular skill area--plumbing, electrical, construction, etc. And they're great at finding problems in that specific area. But sometimes they're not so good at finding problems outside of their area of expertise. And sometimes those are significant issues that the inspector is missing.
Hope that helps.