While all members of the development team did their best to make the software easy to use and bug-free, there are some known issues and limitations in MuseScore 2.0.
'Save Selection...' is currently pretty limited: If the selection doesn't contain a clef, time or key signature, the saved score will be in treble clef, 4/4 time signature, and C major key signature, although all pitches are kept, accidentals added as needed, and even irregular measures are kept.
The local time signature feature, which allows you to have different time signatures in different staves at the same time, is very limited. You can only add a local time signature to measures that are empty, and only if there are no linked parts. When adding notes to measures with local time signatures, you can enter notes normally via note input mode, but copy and paste does not work correctly and may lead to corruption or even crashes. The join and split commands are disabled for measures with local time signatures.
With linked Standard and Tablature staves, if multiple note chords are entered in the Standard staff, each chord should be entered from its top note to the bottom, otherwise the fretting automatically assigned note by note in the Tablature staff may be unexpected (Note: This does not apply to a) note input directly in the Tablature staff nor to b) note input in a Standard staff not linked to a Tablature: in both cases entry order is indifferent).
An instrument change does not change transposition, should any of the instruments involved require that. If this is needed, it is necessary to use different staves and the 'Hide empty staves' option.
Actually there is no real instrument change, just a change of the sound, so not only transposition is not taken into account but also the instrument's range, and the part's name is left unchanged.
Changing values in the mixer does not mark the score 'dirty'. That means if you close a score you may not get the warning "Save changes to the score before closing?". Changing mixer values are also not undoable.
There is no way to edit Header and Footer in a WYSIWYG manner. The fields in Style → General → Header, Footer, Numbers are plain text. They can contain "HTML like" syntax, but the text style, layout, etc. can't be edited with a WYSIWYG editor.