Something people forget is how much the environment can mess with a scanner. A dusty lens or weird lighting can throw off the data before it even processes. That might be what your gut noticed without you knowing why. Angelap56 is right to double-check the physical thing, but also check the physical space where you scanned it. The machine might be fine, but the conditions weren't.
Oh man, you are so right about that. I had a scanner at work once that kept giving me weird results on a batch of parts. I kept cleaning the lens and it still messed up. Then I realized the fluorescent light above it was flickering just enough to mess with the scan every few minutes. Swapped the bulb and boom, everything was fine again. So yeah, dust and lighting are major sneaky problems. It's crazy how small stuff like that can trick your gut before you even put two and two together.
Verify scanner data with physical inspection when possible. Machines can glitch or have outdated calibration. Your gut might pick up on subtle cues the scanner misses. I learned this after a misread caused a small delay in my work.