Grey bars & weird beaming

It's probably not a problem with the MuseScore program but more likely that the scan from PDF to XML was imperfect.

1] By "grey bars", do you mean the minus signs? Those indicate that the total duration of notes in the measure is less than the indicated time signature - they are just indicative, and not elements of musical notation.

2] Weird is in the eye of the beholder but in this case is likely due to the measure being incomplete - i.e. the note's don't add up - so the normal beaming rules don't give you the appearance that you want.

3] By default, MuseScore does not insert notes but replaces rests or existing notes with a new note. When you add a dot to lengthen a note, the time it needs gets taken from the rest or note after it. There are ways to insert notes but the default behaviour is fairly fundamental to the way MuseScore works and it works well in the majority of cases.

The bottom line is that this is probably due to a poor scan interpretation generating a poor XML and that MuseScore is likely just doing its best to interpret this poor XML file. Only very clean scans seem to do OK when interpreted and triplets, in particular, seem to be problematic (such as in measure 49).

For a fuller analysis, you should post original PDF, the XML that your program created and the MuseScore file.

Yes, the small gray bars at the upper right of a particular measure are minus signs. They indicate that the measure is shorter than the time signature says it should be.

From m.14 on, they are mostly (!!!) because you have 2/4 measures, but at 14 it has a Common Time signature (4/4). My first idea was to simply delete that but there are several measures that are other than 2/4, so you can't do it THAT simply.

M. 23 has an "Actual duration" of 7/16. Right-click on the measure (not on any note/rest, but on blank space within the measure) and click Measure properties... from the context menu that appears. Change the Actual duration to 2/4.

Then correct the missing dot. Ctrl+X (Cut) all of that measure except the eighth note at the beginning. Click that eighth note to select and press the period ( . ) key to change it to a dotted eighth. Then select the sixteenth rest after it and Ctrl+V (Paste) the rest of the measure back in.

M.s 41, 46, 51, and 59 have the same issue. Correct them the same way.

M. 50 has six eighth notes and an "Actual duration" of 48/64. Divide by 16 and it is 3/4. This measure clearly should be two eighth note triplets, like the two measures before it. You'll have to actually delete them and add triplets. You may find it easier to add a measure, add the triplets in the blank measure, and then delete the incorrect measure.

At this point, I deleted the Common Time signature and the whole piece is now in normal 2/4.

Cem Anos De Choro-2.mscz

I'm suspicious of m. 43-45. I'm'a guess that that's supposed to be two measures of eighth note triplets rather than three measures of eighth notes. If so, you'll have to fix that; I did not.

If it's supposed to be in Common Time from 14 on, change that back once you fix m. 43-45 and it will separate the measures properly. I did not do that because of those measures.

[A few moments later] Oh, BTW, there is also a gray plus sign that can appear in the same place as the gray minus signs. You can probably guess that it means that a measure is longer than the time signature would indicate.