This happens mostly when the appended files has more tracks than the file it's being appended to. In that case the GUI cannot really find a good place where to place the superfluous tracks, and it ends up laying them out in way that the superfluous tracks would be appended to the last non-superfluous track of the appended file.
You'll have to deactivate those appended tracks for which there's no corresponding track in the file they're appended to.
Example: Let's assume your first file contains one video, one audio track, and that your second file (the one you're trying to append to) contains one video, one audio and one subtitle track. In such a setup the GUI will set up things this way by default:
- the video track from file 2 will be appended to the video track from file 1
- the audio track from file 2 will be appended to the audio track from file 1
- the subtitle track from file 2 has no corresponding track in file 1, but it must be placed _somewhere_; in this case it'll likely be appended to the audio track from file 1, to which the audio track from file 2 is already appended
In that case you'd have to deactivate the subtile track from file 2.