Was it the taffy pit scene? I remember it being very unsettling even with the taffy pit/monster singing (because of course he got a song too like everyone else). I mean, he was self-cannibalizing himself constantly. NIMH doesn't deserve to be mentioned in the same breath as it's actually quite good, however I found the scene with the tractor upsetting the first time I watched it. Classic Bluth was terrifying but beautiful and it was amazing. He respected that his young audience could handle what he threw at them, so long as there was a happy ending.
You freaked out at the tractor scene? Pussy. The scene with the Great Owl was a flat out horror movie. I don't know how Mrs. Brisby expected to get out of there alive but it established how far she was willing to go for her children.