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.x.
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.
Regroup Rhythms command found under the Layout menu may have unintended side effects, including changing the spelling of pitches and deleting some elements like articulations, glissandos, tremolos, grace notes and, esp. on undo, ties. Use this tool with caution on limited selections, so that you can tell if any unwanted changes are made.
When entering multiple-note chords on a standard staff in a linked staff/tablature system, the notes should be entered in order from the top (first) string to the bottom string to ensure correct fret assignment.
This limitation does not apply if entering notes directly onto a tablature staff, or when using an unlinked staff/tablature system.
Changing settings in the mixer other than the sound doesn't 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.