Sam not only received half his money but a note as well.

是的,not only...but also...结构中的前后两个部分必须是平行结构,第一个句子中前面是动宾结构,而后面是名词,所以不是平行结构（或者说对等结构）.
一下两个句子都是正确的：
Sam received not only his money but (also) a note as well.
Sam not only received his money but (also) received a note as well.