That is actually the main reason that both thin and thick washers exist...to make adjustments for proper installation of nuts.
The standard guideline is that up to a maximum of three washers is allowed to be used on a fastener The can be mixed between the bolt head end and the nut end).
If you need more than three, you should change to the next shorter bolt/fastener.
If you need to turn the bolt instead of the nut during installation (to be avoided but sometimes there is no other way) it is a good practice to have at least a thin washer under the bolt head.