I have found that if you import a midi file into a notation editor, they generally will treat the first note as the first note of the first bar because midi doesn't flag up upbeats. This means you usually have to tell your notation editor in some way that there is an upbeat and tell it to adjust the bar lines accordingly.

One way to do this is to pad the beginning of the first bar with rests. I use Noteworthy and that has a function called "Audit Bar Lines" which will make the appropriate adjustment. You can end up with messy notation though, because of the bar lines initially being in the wrong place and notes then straddling bar lines. When the bar lines are adjusted you are often left with pairs of tied notes where a longer note of equivalent total value would be correct.

Midi files are able to store the time signature, (and bar lines) but if the creator of the original file forgets to add a time signature, then most notation editors will default to 4/4. The same is true of key signatures, midi files can store them, but if they are left out the default is Cmaj with all sharps/flats displayed as accidentals.

I often find the best thing is to pad the first bar with rests, insert time and key signatures if necessary and then export the file back to midi and re-import it. That usually sorts things out.