In the Law of God, there are explicit prohibitions on incestuous relationships, for instance:
Leviticus 18:9
9 The nakedness of thy sister, the daughter of thy father, or daughter of thy mother, whether she be born at home, or born abroad, even their nakedness thou shalt not uncover.
Also see Leviticus 18:6-18, 20:11-21, Deuteronomy 22:30, 27:20-23, and 1 Corinthians 5:1 for clear prohibitions on incest.
However, critics of the Bible point to the fact that these kinds of incest were committed by good characters in the Bible, for instance:
Firstly, notice that all of the above instances took place before the Law concerning incest was given. God didn't give the laws concerning incest when the population of the planet was smaller, because there was a smaller pool of people to marry - or in Adam and Eve's children's case - no pool beyond siblings whatsoever.
In the early days of mankind, when peoples' genetic code was nearer to the original, perfect code given to Adam, this would not have manifested the same birth defects that incest results in today. The reason birth defects result from incest today is that closely-related parents are likely to be carriers of the same disease-causing recessive alleles - corruptions that early humans wouldn't have been as likely to have. In a normal relationship though, at least one parent would have a dominant, healthy allele to override the recessive, disease-causing allele. With two diseased recessive alleles, the child will definitely have the disorder.
So, the first reason that this is not a contradiction is because God had not yet told most of those in question not to do it, and had created a situation in which it was not immediately detrimental to someone's health. These days, it's normal for us to wince at incest, because the only reality we know is where it is taboo, prohibited, and dangerous. That wasn't always the case.
Secondly, an account of someone doing something in the Bible is not an endorsement of that behavior - no matter who the character in question is - save Jesus Christ - which should be common sense. The inclusion of what Lot did, for instance, as somehow being an endorsement of incest, is just dishonest, and ridiculous.
I could show you an example of Moses killing someone for a non-capital offense (Exodus 2:11-12). Does that mean that the Bible contradicts itself on whether murder is prohibited? No, it means Moses contradicted the Law of God, which is called a sin (1 John 3:4). There are thousands of examples of people sinning in the Bible.
The Law concerning incest was given at a specific point in human history for a reason. Prior to that, it was not a sin. Even if it was, an account of someone sinning is not an endorsement of that sin, as is evidenced by thousands of verses of Scripture, and common sense.
Also, recognize that everyone, even today, marries a relative. If you aren't marrying a relative, you aren't marrying a human being. No matter who your spouse is, you both share quadrillions of names in your family trees, as anyone who has made a family tree will be able to deduce. Of course, those names are not all unique, because everyone has relatives that are included scores of times each, further demonstrating the point. It's only intermarriage between close relatives that results in problems, though, and so that's why God prohibited it, and the Bible is consistent on that point.