A few inconsistencies that come to mind are the two witness rule, their blood policy, and their stance against IVF and gestational surrogacy.
The Borg requires two witnesses to child sexual abuse before even reporting the accusation to secular authorities for a proper investigation, unless the legal department tells them it's required by law. On the other hand, purely circumstantial evidence, such as staying overnight under "improper" circumstances, is considered proof enough to take judicial action on the assumption that horizontal hanky-panky must have taken place.
Blood transfusions involving plasma or "whole blood" are absolutely forbidden, though almost every single component of blood and most blood fractions can be used separately. It's like saying ham sandwiches are forbidden, but you can have all the bread, ham, tomato, lettuce, and condiments you want as long as you eat them separately.
Even if one concedes that blood transfusions are prohibited "in principle," there are specific examples in the Bible where people actually ate unbled meat in an emergency and received only a virtual "slap on the wrist" as punishment. Accepting a blood transfusion is not the same as eating blood anyway. Regardless, the Bible clearly shows that saving a life justifies breaking the rules. Jesus himself used the example of violating the Sabbath in order to save an animal's life, confirming that it was acceptable to do so. Having one actually die in order to acknowledge the sanctity of life is ludicrous and contradictory. It elevates the symbol above the reality. Saving a life is more important that obeying any specific law, just as life itself is far more sacred than something that merely symbolizes it.
The Borg's blood policy is one example of taking the principle behind a Jewish dietary law and turning it into an eternal law from God that applies to modern medical procedures that are not in fact equivalent anyway. But then they go to the opposite extreme and completely ignore explicit Biblical precedent and impose their own interpretation of what constitutes adultery when it comes to IVF and surrogacy. They equate the donation of sperm or human eggs from anyone other than one's spouse with adultery. The same with a woman who bears a child not biologically related to her for another couple. This completely ignores the brother-in-law marriage laws of the Hebrew Scriptures (Old Testament). In those days, if a married man died without an heir, his brother (or other close relative) was required to impregnate the dead man's widow. Obviously, this involved actual sexual intercourse, not merely the clinical transfer of biological material from one willing person to another. The child born of this brother-in-law procedure was considered the legitimate heir of the dead man. The act was not considered adultery in any sense. In fact, there were humiliating penalties for not complying with this law. As for surrogacy, one need only consider that Abraham's wife Sarah had him impregnate Hagar (her hand maiden) so that she (Sarah) could have a son. This, too, involved actual intercourse but was not considered adultery.
This clearly shows that sperm or egg cells are not, in and of themselves, sacred. Otherwise, why were men's bodies designed to naturally and automatically dispose of excess semen while they sleep? And why were women's bodies designed to naturally and automatically dispose of unfertilized eggs during their monthly cycles? Adultery is about unfaithfulness to one's mate, usually involving deceit and disloyalty, not merely the transfer of biological material. In my opinion, IVF procedures and surrogacy constitute the greatest gift one person can give another. All parties involved have given willing, informed consent. Based on the principle and precedent of brother-in-law marriage, how can that be called adultery?