You got my attention there, what do you mean? I don't see a problem with those instances, but I'll elaborate why in a second. First, I want to get this out of the way cuz I think it could lead to some misunderstandings.
There are 4 "typical" ways 2nd inversion triads are used:
In the context of a Tonic-Dominant cadence with a 4-6 suspension. In this case the cadence is towards C major, the entire measure would be seen as "dominant," yet anatomically the first beat is 2nd inversion C major. It's only "ignored" due to it being a suspension.
As a passing note (in this case the middle chord would be 2nd inversion G major.) Note how it's also in a non-accentuated beat.
As a consequence of a sequence of inversions within the same chord. Note that as the bass spells out the triad, it will inevitably pass through the 5th.
And finally as a result of a pedal note.
Now, all that being said, I think that if you're only using two voices, there's a lot more room to change up the voice movement without it implying necessarily an inversion. However, this all really depends on how much you want to adhere to typical conventions. You can try different alternatives to using 2nd inversions, see if they sound better to you. There's no hard fast rule for this since there are plenty of exceptions anyway.