sounds like "container stress"....in other words...water logged without roots in a cube or rooter....sometimes when you root cuts the trunk and leaf stems will turn deep red....it is a stress thing....if you planted them into pure roots with clean water, they will grow out of it after the first week.....my cuts often do this.....as a matter of fact, all my last cuts turned red to some degree....and are all perfectly normal colored two weeks after transplant into base soil....