Continuity mistake: At the end of the town collapse, a sincerely drunk Ben dives head-on into a tub where a lady (in her underclothes?) is just enjoying a bath. Propelled by Ben's momentum the tub with both passengers slides down the slippery planks and splashes into the river, while Ben rearranges himself into a comfortable sitting position between shots. If I wasn't completely mistaken also the lady changes her outfit, since the embroidery is missing when they float along.
Revealing mistake: In the climactic scene when the whole town ends up in Ben's and Pardner's tunnel system, including the brothel where young Horton is once again exploring his limits, the bed with Horton and his lady of choice falls on the street. When it topples over it's obvious that both Horton and his sparring partner are tied to the bed.
Revealing mistake: In the scene where the town is collapsing, there is a shot of Ben in the bathtub falling into the river, if you look closely, you can see the strings that are keeping the tub steady and upright.
Continuity mistake: When Lee Marvin hits Clint Eastwood and interrogates him about riding the same horse with Elizabeth, Marvin's chin strap alternates begins the scene tucked tightly under his chin, then is resting against the front of his face, then tucked under his chin again, yet he never touches it with his hands.