If every performer played music exactly as scored, all renditions would be the same. It is the little variations "leaning" on one note and slightly cutting another that makes for the interesting and often wonderful interpretations of music. As has already been said, MIDI notation allows for very fine control of note length and if a notation program is trying to translate a live (or simulated live) performance MIDI, this will happen. My ex-wife was a professional musician and when she entered music via a midi keyboard, there would always be the extra double-dotted notes, 1/32 notes and rests etc.

My music program "Personal Composer" allows me to define the shortest note to be used when taking input from a MIDI file or input device and setting this to a semi-quaver (1/16) will often sort this out. Triplets and other tuplets will often confuse notation programs, especially if they contain dotted notes. Most MIDI files which have been produced by a notation program will load accurately into another, provided they weren't produced with a "Swing", "Loose" or other interpretation feature.

Any choral singers who are looking for MIDI files to learn parts from etc. might be interested in The Silvis Woodshed which even includes some of my files.