MicroRNAs (miRNAs) are a widespread class of regulatory noncoding RNAs with key roles in physiology and development, conferring robustness to noise in regulatory networks. Consistent with this buffering function, it was recently suggested that human miRNAs coevolve with genes in copy number regions (copy number variation [CNV] genes) to reduce dosage imbalance. Here, I compare miRNA regulation between CNV and non-CNV genes in four model organisms. miRNA regulation of CNV genes is elevated in human and fly but reduced in nematode and zebrafish. By analyzing 31 human CNV data sets, careful analysis of human and chimpanzee orthologs, resampling genes within species and comparing structural variant types, I show that the apparent coevolution between CNV genes and miRNAs is due to the strong dependency between 3'-untranslated region length and miRNA target prediction. Deciphering the interplay between CNVs and miRNAs will likely require a deeper understanding of how miRNAs are embedded in regulatory circuits.