I've never tried exporting musicXML, but importing musicXML to Logic sometimes represents things differently from the original content, leaving out some high notes (even though they are well within the tessiatura), notes which would be imported perfectly as MIDI, and refusing to playback articulations, even though they clearly get imported. (Maybe recent versions have fixed some of these issues.) My version is 10.5.1, versions some time before that didn't really appear to support functional musicXML so hopefully your version is more recent. The jumbled lines in your PDF looks like a glitch, such that there's some part in the music which is messing everything up. You might try cutting parts of the music, cutting half of the parts away, or cutting some of the parts away to see if the glitch is caused by some specific part. Wish I had a better tip.
For the vibraphone notes showing up wrong, are you sure (1) the vibraphone is not marked as a transposing instrument (if there is such a feature in Logic), and (2) how about when you use a 8va clef, which is sometimes necessary for the music to be readable?