No, it doesn’t. Parts of the Torah are shocking by design. The feeling of discomfort itself is not a failure. It’s how you handle it that matters.
If you immediately try to reconcile the conflict by re-interpreting the Torah to fit your pre-established narrative, sure, that’s a big problem. But you could respond in a number of different ways.
You could say, Clearly I didn’t understand this properly, let me keep working through it until I do understand (without any agenda at hand, just reading through all the commentaries and going over it multiple times). Or you could ask yourself, Why is it that I have this discomfort? Where is that stemming from, and how can I deal with it? Or you can say, I see that I am uncomfortable, I accept that I am uncomfortable, I choose to embrace the Torah despite my discomfort, to acknowledge the discomfort and then to set it aside.
Etc, etc.