It's made heavily clear she has felt guilty for so long, and lived with the guilt by putting up a facade.

The monsters used in the experiments were willing donations by the families, and they were all on their deathbeds. Alphys was trying to see if she could prevent death through using Determination, and at first it seemed like it worked and she was glad to let the monsters return home safe and happy.

However of course she couldn't have known things would go wrong, so much so she felt like a total fraud and failure. She still tried what she could by caring for the amalgamations so at least they were not in too much pain, but once she finally was able to admit to her faults she let them go and reunite with their families, and in the end it's shown the families, while surprised, still accept the relatives they once thought dead, likely forgiving Alphys for something she could not have predicted would happen.

In all fairness she also engineered a semi life threatening scenario so she could feel good about herself and a bused her friendship with metaton to do it
So even if you don't see her as the monster Mengala, she's still a bit of a jerk