I use the easy angle ruler and my squares end up being the right size. Maybe thats becuase the instructions for our BOM were written really good. Thank goodness for local quilt shops.
If you have a lot cut - you have two choices trim the squares to the size of the 1/2 square triangle pieces or cut and make new triangle pieces.
Also - I made the same mistake when I started out. But I did not have the terrific board to help me.