Q: Files not shown in folder

Go Finder/View/Show Path Bar. Do the search, select the file, and the file's location should appear in the Path Bar.

In the search window, select the file and press Command-R to see it in the actual folder where it is located. What do you get?

1) Can you open the file?

2) Reflecting on this, there are two major possibilities: either the spotlight index is corrupt or you may have disk directory problems.

You may run Disk Utility in Recovery mode and do a First Aid on your drive, to check for disk issues.

And you can force Spotlight to reindex your drive (system preferences->Spotlight->Privacy; add your drive to the list, and then remove it to force a reindexing).