Howdy,
David is correct about cleaning up rests and other aspects of the notation. You can select which options you want in Setup/Transcription Options (you can also select which types of automatic steps you want done, such as transposing guitar/bass up an octave, or splitting piano tracks into two-staff parts).
Here's a brief overview (you can also look up specific aspects in Help/Users Guide, using the Index to look up "transcription" and then selecting the specific topic of interest to you.)
TranscriptionOptions.png
You can also see a short Tutorial Video of these options and what they do in the
Transcription Options video (click here to go there 
).
Enjoy!
Sherry