Musescore not deleting instruments, bars messed up and key signatures changing

The other day I started a skyrim theme song composition for my school band so downloaded a template to help me out, the template worked ok but whenever I would try to delete an instrument we didn't have from the score musescore would crash. So I thought that I could just copy and paste all the stuff of the template onto a new score with the correct instruments on it, but whenever I would create a new one the whole rests would appear in the middle of the bar lines, the trumpet would have one too many sharps, and the paper had to be tripled in size to be able to see all the instruments I was using (about 15). I don't know why this is happening, please help.