Some unaccounted for rests appearing

It looks like those whole rests belong to another voice that's not being actively used.

Try clicking on one of the rests in question, and then look at the little colored grid at the rightmost end of the Note Entry Toolbar (with rectangles labeled 1, 2, 3 and 4).

When you select notes or rests in different voices, it will be reflected appropriately in that grid by a change in which rectangle is highlighted.

Assuming that those whole rests are in voice 3, you should see the yellow rectangle labeled "3" become highlighted when you select one of them.

If you don't anticipate adding a third voice in those measures, you should be able to delete the rests or make them invisible by right-clicking and selecting Set Invisible.

Recall that you can use up to four voices in your treble clef and another four in your bass clef. In both cases, they have the same numbers and colors.

I'm guessing that when you went directly to voice 3 when entering the bass clef, there were already rests there in voice 1 that you may not have noticed at the time.

The conventional logic of creating a polyphonic score with two voices notated in treble and two voices in bass would be to use voices 1 and 2 of the treble clef and voices 1 and 2 of the bass clef -- i.e., employing each successive voice in numerical order for each staff -- though it doesn't seem to be strictly necessary.