Extremely low p-values from non-parametric tests
You do not need to worry about something going wrong with the scipy functions.  P values that low just mean that it's really unlikely that your samples have the same parent populations.
That said, if you were not expecting the distributions to be (that) different, now is a good time to make sure you're measuring what you think you're measuring, i.e. you are feeding in the right data to scipy.
I'm using Python's non-parametric tests to check whether two samples are consistent with being drawn from the same underlying parent populations: scipy.stats.ks_2samp (2-sample Kolmogorov-Smirnov), scipy.stats.anderson_ksamp (Anderson-Darling for k samples), and scipy.stats.ranksums (Mann-Whitney-Wilcoxon for 2 samples). My significance threshold to say that two samples are significantly different from each other is p = 0.01.
If these three tests return extremely low p-values (sometimes like 10^-30 or lower), then do I need to worry about something having gone wrong with the scipy functions? Are these ridiculously small p-values reliable, and can I just report p << 0.01 (p much less than my threshold)?