Considering that the plow went over an entire Virmen, uprooting them and all that, a single additional click on the recently disturbed plot of dirt after the commotion is not unexpected.
I agree with the OP. I had the exact same concerns when I first tested this, and thought it was a bugged when it didn't plow the dirt under the vermin. It seems counter productive to have to go back and do it again. The purpose of this new system (I assume), is to save time, and make farming more convenient. It is actually the opposite.
It's still faster and easier to just click through all the vermin available in the 16 slots, gather them up, kill them, THEN plow through the 4 lines at a time, without having to go back.
The new way, I have to plow a line, kill 1 or 2 vermin, click their plots to till the soil, then rinse and repeat 3 more times.
It's easier to just kill all the vermin at once.