Hidden pauses

Please post the file so we can see what the problem is.

I suppose you used the MuseScore import pdf function which uses the Audiveris music recognition engine.
If so and my experience is better to install the Audiveris program on your computer. If you then run a music recognition using Audiveris stand alone program, you can correct and remove "junk" before you open it in MuseScore. The recognition quality may not be better, but it's easier to correct things on Audiveris level than in MuseScore

I will write in Russian and English.
Мое мнение - лучше вообще не использовать фукнцию импорта pdf. Она очень плохо работает, и время, которое вы потратите на исправления, лучше потратить на набор нот.
Можно сделать и так, как посоветовал комментатор выше - поставить audiveris. Но результат будет не сильно лучше.
Поскольку audiveris генерирует musicxml, вы получите дополнительные ошибки на импорте в Musescore.

My opinion is that it is better not to use the pdf import function at all. It works very poorly, and the time you spend on corrections would be better spent on typing notes.
You can also do as the commentator above advised - install audiveris. But the result will not be much better.
Since audiveris generates musicxml, you will get additional errors when importing into Musescore.