There are plans to have synths of the same location link together automatically, but I don't know whether that applies to putting the fractured pieces of a single synth back together or not.
If you switch to Grid Mode (use the second icon from the right and choose 'Images' - or alternately just press the tilde key after clicking the synth with your mouse - the tilde key looks like this [~] ) you can easily see which images Photosynth was able to link together by the groups that they appear in within Grid Mode.
The smallest images at the bottom of Grid mode are ones that didn't match any other images.
Looking at the % synthy score of a synth will give you a good idea of what percentage of the photos matched each other. For example, in a synth with more than 100 photos, one or two photos might not match but if all the others do, the synth will still receive a score of 100% synthy because each photo now counts for less than 1% of the total number of photos.