Difference in Pitch Causes Dissonance

See https://musescore.org/en/handbook/soundfonts-and-sfz-files. Basically, there are imperfections in the default sound set that can create this effect. A SoundFont like TimGM6mb will have very pure pitches, but there is a trade-off in realism.

MuseScore is a tool for notating your composition; it will notate almost anything you can imagine, but it cannot 'address the issue' of the composer specifying dissonant intervals. That is up to the composer.

General rules for composition:

1. Write your bass line first, then write the melody to fit it
2. Use contrary or oblique motion between voices wherever possible
3. Use parallel motion ONLY in thirds, sixths, or tenths, and for limited lengths of time (half a measure or less)
4. Avoid intervals other than thirds and sevenths (and the inversions thereof) until you know what you're doing
5. Avoid 6/4 chords except at cadences or those which result from suspensions
6. Don't modulate to a key other than the dominant or the relative minor until you understand how to get back to your home key
7. Stick to major keys until you understand them perfectly; writing in minor is much more complex
8. Don't try to write in more than three voices until you have mastered that species.