An mstidx file was apparently being used by another process. The resource in question was Novum Testamentum Graece (LLS:1.0.323), which moments before I had moved into hidden resources.
Logs attached.
7608.Logos4Indexer.log
1351.Logos4IndexerCrash.txt
I've submitted your crash report. Thanks.
Update: This will be fixed in the next beta. If the file can't be deleted, we will just leave it on disk. (It will consume a small amount of space, but not hurt anything to leave it there.)