Due to tolerances and such, M3 must extend beyond the ends of the mim cap

as for the first error, that is just a via to layer tolerance issue. The mim contact must be placed on top of the mim cap layer. Due to tolerances in manufacturing it must be placed more than 0.08um from the edge of the mim cap layer

I dont know how you are creating the device in magic, but you need to have the mim layer be at least 0.14um in all dimensions than the M3 layer and the mim contact layer be at least 0.08um smaller in all dimensions.

You can use the box shrink command if you are drawing the area manually. For example:

box 0um 0um 5um 5um 
paint m3
box shrink center 0.14um 
paint mimcap
paint m4
box shrink center 0.08um 
paint mimcapcontact

should draw a DRC clean cap with an electrode area of 4.72x4.72um