I'm not sure what to do about (1), but (2)-(5) are due to your repeat. The 
right brace of the repeat should contain all the alternative endings (the newer 
syntax), and there should be nothing else in \alternative besides those 
endings. If you do have something else, it should be moved into one of the 
voltas.

Music = {
 b'1
 \break % to show colored bar line
 \ColorRepeatBegSpecialBar
 \repeat volta 2 {
  c''1 |
 
 \alternative {
  \volta 1 {
   d''1 |
   \ColorRepeatEndSpecialBar
  }
  
  \volta 2 {
   e''1 |
  }
 }
 }
}

As for (1), i think lilypond considers them to be the same barline, though I'm 
not totally sure.

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