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Why are barlines misplaced and rhythms incorrect?

These types of files are typically due to "metronomeless" recording, and can be corrected using Notation Composer's (https://www.notation.com/NotationComposer.php ) "ReBar" feature ( https://www.notation.com/Tutorial%20Videos/ReBar/ReBar.mp4 ).

Notation products do an excellent job interpreting the rhythms of notes in MIDI files, even if the notes are not "quantized". As long as the author of the MIDI file recorded notes on his MIDI keyboard (or other device) in synchronization with a MIDI metronome ("click track"), then Notation will be able to interpret the rhythms, even though the recorded notes inevitably will not be precisely on the beat.

Note, however, that some MIDI files are recorded without reference to a metronome, that is, without use of a "click track". Notation cannot correctly analyze the rhythms in such MIDI files, nor can most other music notation programs.

You can tell whether a MIDI file has been recorded without reference to a metronome by following this simple procedure. After your Notation product has opened the MIDI file, start playback. Watch the vertical playback cursor (blue, by default) move along with the playback. Listen to playback and start tapping the beats with you hand or foot. Does the playback cursor move in synchronization with the beats you hear? If so, the MIDI file was indeed recorded with reference to a metronome. If the beat movements of the playback cursor do not relate to the beats you hear, then the MIDI file was recorded without reference to a metronome, and there is no way in the current version of Notation to produce accurate rhythms in the score.

Notation Composer now has a ReBar feature that allows you to adjust the barlines and beats of such music files so that you can still have the typically fabulous "live" sound, and still get good sheet music.  Please see in the User Guide under the Index search for "rebar".  You can also see a Tutorial Video at https://www.notation.com/TutorialVideos.php