As far as I understand you simply don't have to worry about that.
So, you have a sample split randomly in control and treatment. You measure something before treatment, and after, for the same individuals. Because you measure on the same individuals than you have paired measures: delta = before - after. You are interested to measure if the mean of delta for control sample is significantly different than the mean of delta for control sample. This is done with paired sample test known also as dependent test.
If you assume a normal distribution you can use paired t test. If you can't reasonably assume the normal distribution than you can use Wilcoxon signed rank test.
The idea of pairings in test is to eliminate the effect of confounders. What you computed can be the effect of a confounder, but if the sample was split randomly in control and treatment you should not worry about that, unless you have strong reasons to doubt the randomization procedure. In the later case you perhaps should include confounders in the equation and take the route of random effects modeling.