I keep getting messages that say "Index.xmi.file missing"

Are there particular applications or tools in use when the error is generated?

The quoted message is not at all common, but there's a very similar "index.xml file is missing" error that can arise with iWork documents.

If this is iWork, which version(s) are in use? Documents that were written out using iWork 9 (by default) have some changes that iWork 8 can't deal with, for instance. If you have it, can a system running iWork 9 open the document?

Pages '09 and earlier document formats use an internal file named index.xml. All releases of Pages v5 use a different document architecture, and no longer use that internal index.xml file. When you leave Pages '09 running, and double-click a Pages v5 document, you will get this truthful dialog, because you are asking Pages '09 to open an incompatible document format.

Quit Pages '09. Double-click the same document, and it will open correctly in your release of Pages v5.