In this experimental context, does the re-use of a control bias/invalidate the result?

I'm contributing to a paper where I am a fairly minor author. I'm concerned by the experimental design but the corresponding authors, who have decade(s) more experience in the field than I have, seem unconcerned and there's the implication that I'm being unnecessarily picky. I'm 95% sure I'm correct, but given their attitude and the fact that my remaining option is to have my name removed from the paper, I'm chasing that final 5% of sureness. In the first experiment, knocking out a gene was shown to cause a significant increase in cell size (simple t-test). To confirm this phenomenon, they then knocked out another gene involved in the same biological process and showed the same effect (also using a t-test). They then tested another three or four genes more tangentially related to that process and saw a significant effect in some of them and not others (t tests). Due to time constraints and the fact that, at the time, they didn't know if this was going anywhere, these three experiments all compare to the same control. While they've built on this in later experiments, these three experiments are all in the paper and provide the base for the latter experiments. This concerns me. Firstly, we know there’s a lot of variation in the experimental model over time so the control from the first experiment doesn't necessarily control for technical variations in the second two experiments. Secondly, and more importantly, in the second two experiments they compare the effects of disruptin…