What happens to the complementary base when the other undergoes a base substitution mutation?
Consider a stretch of DNA

A T C C T C
T A G G A G


Let's say that during replication a nucleotide get switched

A G C C T C
T A G G A G


Now, this does not work. The cellular machinery will find this location and try to solve it. It will either resolve it as 

A T C C T C
T A G G A G


and no mutation would have happened. Or it will solve it as

A G C C T C
T C G G A G


and a mutation just happened.

You might want to read about DNA repair mechanisms.