Version 2.6.2, and perhaps earlier ones as well, recognize multiple tracks inside a single file. The tracks are automatically clustered, by the file itself, and any release tag (i.e. MUSICBRAINZ_ALBUMID) in the file is used to import metadata for all tracks into the single file (see PICARD-358 and PICARD-1532).

Generally, this mechanism works correctly, as least with respect to features already implemented, but the application behaves strangely for some files, with no plain indication of the cause for the difference. In such cases, the application shows the tracks clustered, in the right-hand pane, but also shows the file itself, separate from the tracks, in a category below, labelled "Unmatched files". It is confusing what this designation might represent, since the only possible reason for the tracks being displayed is that they occur in the file. More, the application will not save the file, in these cases.

So far, I identify no pattern over which files are affected by the problem.

I would try to provide any information helpful for diagnostics, if someone would clarify what is needed.