That's rather spurious. Are you sure that everything is really on the timeline? What throws some users, is the expectation that for each clip a unique chapter will appear. However, there is a default value of ca 30 seconds, below which shorter clips will simply be joined.

It may then appear that certain clips were excluded, yet they were simply added to other clips so that this arbitrary value was met. If you mean that, try looking at the clips, i.e. chapter menus that you see for your 'lost' clips. Cheers, M o' L.