High notes on bass clef don't work
If I place a middle c on bass clef, it will play just fine. If I place an A note above that c, or just by itself, however (5 steps above) it plays an A note that is one octave lower than what it shows.
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If that is true, it sounds like something is wrong, but no one here can tell exactly what the problem is until you attach that score. Seeing the score will make analysis so much easier than having to guess what the problem might be.
Random guess:
You're using mouse input on a grand staff and haven't actually inputted an A above that C in the bass clef, but a different (low) note on the treble clef above it because at some point in-between those staves MuseScore has to decide whether you're inputting on the lower or the higher staff.